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 14

System / cell line: sequenced ✕ Assay: acid ✕ Clear

Towards the identification of essential genes using targeted genome sequencing and comparative analysis.

PMID 17052348 · PMC1624830 · BMC genomics · 2006 · 8 claims · 8 setups

Full-text index only

Phyletic retention (ortholog presence across organisms) is the single most predictive feature of gene essentiality in both E. coli and S. cerevisiae.

coli cerevisiae comparative machine single-gene
Microbial metagenomics.

PMID 16207365 · PMC1257460 · Genome biology · 2005 · 8 claims · 8 setups

Full-text index only

Metagenomic sequencing of the human GI tract reveals microbial community composition (e.g., Actinobacteria and Archaea prominence) differing from prior culture-based estimates dominated by Firmicutes and Bacteroides

gastrointestinal acid ocean group metagenomic shotgun comparative
A surrogate-based approach for post-genomic partner identification.

PMID 11602024 · PMC57814 · BMC biotechnology · 2001 · 8 claims · 5 setups

Full-text index only

Peptide surrogates derived from random phage display libraries contain amino acid sequence information that identifies the natural biological partner of the panned target via database searching.

biotinylated tnf-β analysis secondary phage sequence secondary
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
Genetic variation of St. Louis encephalitis virus.

PMID 18632961 · PMC2696384 · The Journal of general virology · 2008 · 8 claims · 4 setups

Full-text index only

Phylogenetic analysis of 106 SLEV E gene sequences confirms seven major lineages (I-VII) and refines them into 13 clades (IA, IB, IIA, IIB, IIC, IID, IIG, III, IV, VA, VB, VI, VII)

slev rt-pcr phylogenetic recombination
Comparative genomics and understanding of microbial biology.

PMID 10998382 · PMC2627966 · Emerging infectious diseases · 2000 · 8 claims · 7 setups

Full-text index only

GC content varies widely among prokaryotic genomes (29% in B. burgdorferi to 68% in M. tuberculosis) and shapes codon usage and amino acid composition.

completed same sequenced mycobacterium whole-genome comparative phylogenomic
Genomic sequence and analysis of a vaccinia virus isolate from a patient with a smallpox vaccine-related complication.

PMID 17062162 · PMC1635044 · Virology journal · 2006 · 8 claims · 6 setups

Full-text index only

VACV-DUKE is most similar to VACV-ACAM2000 and VACV-CLONE3, confirming it as a Dryvax-derived isolate

vacv-duke whole-genome phylogenetic comparative
Country-wide assessment of the genetic polymorphism in Plasmodium falciparum and Plasmodium vivax antigens detected with rapid diagnostic tests for malaria.

PMID 18957099 · PMC2582241 · Malaria journal · 2008 · 7 claims · 8 setups

Full-text index only

pfhrp2 and pfhrp3 genes show markedly higher polymorphism than the P. falciparum and P. vivax aldolase and pldh genes

falciparum vivax extracted febrile pcr nested species-specific
Timing constraints of in vivo gag mutations during primary HIV-1 subtype C infection.

PMID 19890401 · PMC2768328 · PloS one · 2009 · 7 claims · 7 setups

Full-text index only

Reverse mutations to the wild type (HIV-1C consensus) in Gag appear significantly earlier than escape mutations from the wild type during primary infection

hiv-1 same sequenced gag single-genome mhc hypermutation
Versatile and open software for comparing large genomes.

PMID 14759262 · PMC395750 · Genome biology · 2004 · 8 claims · 8 setups

Full-text index only

MUMmer 3.0 efficiently handles comparisons of large eukaryotic genomes at varying evolutionary distances

escherichia chromosome drosophila anopheles suffix-tree whole-genome protein-level
Natural history of S-adenosylmethionine-binding proteins.

PMID 16225687 · PMC1282579 · BMC structural biology · 2005 · 8 claims · 6 setups

Full-text index only

The last universal common ancestor (LUCA) of cellular life had between 10 and 20 SAM-binding proteins from at least 5 fold classes

arabidopsis nicotianamine rossmann-fold cyclopropane psi-blast pdbblast comparative
Genome-wide diversity and selective pressure in the human rhinovirus.

PMID 17477878 · PMC1892812 · Virology journal · 2007 · 7 claims · 6 setups

Full-text index only

Whole genome and subgenomic phylogenies of HRV are essentially identical at every locus, indicating consistent phylogenetic patterns across the genome.

diverse hrv fully hrva genome phylogenetic pairwise
Multilocus sequence typing of Cronobacter sakazakii and Cronobacter malonaticus reveals stable clonal structures with clinical significance which do not correlate with biotypes.

PMID 19852808 · PMC2770063 · BMC microbiology · 2009 · 8 claims · 6 setups

Full-text index only

A seven-locus MLST scheme (atpD, fusA, glnS, gltB, gyrB, infB, pps) reliably identifies and discriminates C. sakazakii and C. malonaticus strains

sakazakii cronobacter sequenced multilocus biotyping phylogenetic
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

Full-text index only

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

Towards the identification of essential genes using targeted genome sequencing and comparative analysis.

Microbial metagenomics.

A surrogate-based approach for post-genomic partner identification.

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.

Genetic variation of St. Louis encephalitis virus.

Comparative genomics and understanding of microbial biology.

Genomic sequence and analysis of a vaccinia virus isolate from a patient with a smallpox vaccine-related complication.

Country-wide assessment of the genetic polymorphism in Plasmodium falciparum and Plasmodium vivax antigens detected with rapid diagnostic tests for malaria.

Timing constraints of in vivo gag mutations during primary HIV-1 subtype C infection.

Versatile and open software for comparing large genomes.

Natural history of S-adenosylmethionine-binding proteins.

Genome-wide diversity and selective pressure in the human rhinovirus.

Multilocus sequence typing of Cronobacter sakazakii and Cronobacter malonaticus reveals stable clonal structures with clinical significance which do not correlate with biotypes.

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.