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 13

System / cell line: each ✕ Assay: support ✕ Clear

Bushes in the tree of life.

PMID 17105342 · PMC1637082 · PLoS biology · 2006 · 8 claims · 8 setups

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Bush-shaped clades, produced by short internal stems and long external branches, resist phylogenetic resolution regardless of the amount of conventional data collected.

chimpanzee elephant coelacanth metazoan multi-gene rare nuclear
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
An enhanced single base extension technique for the analysis of complex viral populations.

PMID 19834618 · PMC2759544 · PloS one · 2009 · 8 claims · 7 setups

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The MDAP single base extension microarray platform measures nucleotide frequency at each genomic position in a complex population without requiring prior knowledge of candidate SNPs

transcribed poliovirus array-bound array single oligonucleotide sbe
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
Genome-wide signatures of convergent evolution in echolocating mammals.

PMID 24005325 · PMC3836225 · Nature · 2013 · 8 claims · 8 setups

Has reproduction

Genome-wide convergent sequence evolution between echolocating lineages is not rare but widespread and continuously distributed, with signatures consistent with convergence in nearly 200 loci out of 2,326 examined.

four raw orthologous mammalian whole-genome novo homology-based
Ordinal-level phylogenomics of the arthropod class Diplopoda (millipedes) based on an analysis of 221 nuclear protein-coding loci generated using next-generation sequence analyses.

PMID 24236165 · PMC3827447 · PloS one · 2013 · 8 claims · 8 setups

Has reproduction · 82

An ordinal-level phylogeny of Diplopoda reconstructed from 221 nuclear protein-coding loci (61,641 aligned amino acid columns) differs from existing classifications in fundamental ways.

exemplar paired-end cleaned assembled transcriptome read novo
Comparative genomics of the syndecans defines an ancestral genomic context associated with matrilins in vertebrates.

PMID 16620374 · PMC1464127 · BMC genomics · 2006 · 8 claims · 6 setups

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Syndecan-encoding sequences are present in Cnidaria and throughout the Bilateria, showing deep conservation of the family.

invertebrate syndecan full-length chicken wu-blastp clustalw tcoffee
Distinctive pattern of sequence polymorphism in the NS3 protein of hepatitis C virus type 1b reflects conflicting evolutionary pressures.

PMID 18632963 · PMC2577380 · The Journal of general virology · 2008 · 7 claims · 6 setups

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NS3 shows less evidence of purifying selection acting on its CTL epitopes than the other 9 HCV proteins, while outside the CTL epitopes NS3 is more conserved than the other proteins.

complete hcv-1b sequence nonsynonymous comparative neighbor-joining maximum
A target enrichment method for gathering phylogenetic information from hundreds of loci: An example from the Compositae.

PMID 25202605 · PMC4103609 · Applications in plant sciences · 2014 · 8 claims · 8 setups

Has reproduction · 87

A custom sequence capture probe set (9678 baits targeting 1061 orthologous genes) was designed to enrich COS loci across the Compositae.

compositae same species helianthus targeted genome genomic
Genomic organization and recombinational unit duplication-driven evolution of ovine and bovine T cell receptor gamma loci.

PMID 18282289 · PMC2270265 · BMC genomics · 2008 · 8 claims · 6 setups

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The sheep TRG1 and TRG2 loci evolved through a series of duplication events involving either entire V-J-J-C recombinational cassettes or single V genes

sheep bac dot tandem
Tandem repeats modify the structure of human genes hosted in segmental duplications.

PMID 19954527 · PMC2812944 · Genome biology · 2009 · 8 claims · 6 setups

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Around 7% of primate-specific genes located within segmental duplications contain variable internal tandem repeats (ITRs).

genome genomic est paired genome-wide comparative cnv
Swarm intelligence based wavelet coefficient feature selection for mass spectral classification: an application to proteomics data.

PMID 19733729 · PMC2748225 · Analytica chimica acta · 2009 · 8 claims · 4 setups

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ACA-based wavelet coefficient feature selection can achieve up to 100% classification accuracy on training, validating, and independent testing sets using only 5 selected features.

blood baseline-corrected 953-dimensional training seldi-tof wavelet ant
Genetic variability of the P120' surface protein gene of Mycoplasma hominis isolates recovered from Tunisian patients with uro-genital and infertility disorders.

PMID 18053243 · PMC2225410 · BMC infectious diseases · 2007 · 7 claims · 5 setups

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The P120' surface-exposed N-terminal region undergoes substantial genetic variability among Tunisian M. hominis clinical isolates

cloned clinical hominis pcr culture sanger

Experiments

Bushes in the tree of life.

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

An enhanced single base extension technique for the analysis of complex viral populations.

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

Genome-wide signatures of convergent evolution in echolocating mammals.

Ordinal-level phylogenomics of the arthropod class Diplopoda (millipedes) based on an analysis of 221 nuclear protein-coding loci generated using next-generation sequence analyses.

Comparative genomics of the syndecans defines an ancestral genomic context associated with matrilins in vertebrates.

Distinctive pattern of sequence polymorphism in the NS3 protein of hepatitis C virus type 1b reflects conflicting evolutionary pressures.

A target enrichment method for gathering phylogenetic information from hundreds of loci: An example from the Compositae.

Genomic organization and recombinational unit duplication-driven evolution of ovine and bovine T cell receptor gamma loci.

Tandem repeats modify the structure of human genes hosted in segmental duplications.

Swarm intelligence based wavelet coefficient feature selection for mass spectral classification: an application to proteomics data.

Genetic variability of the P120' surface protein gene of Mycoplasma hominis isolates recovered from Tunisian patients with uro-genital and infertility disorders.