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).

• Versatile and open software for comparing large genomes.

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

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

  escherichia chromosome drosophila anopheles suffix-tree whole-genome protein-level

• Genetic diversity among five T4-like bacteriophages.

  PMID 16716236 · PMC1524935 · Virology journal · 2006 · 8 claims · 8 setups

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  A core set of 82 conserved genes (T4-like genes) is present in all five genomes analyzed, clustered in large collinear blocks.

  bacteriophages five conserved aeh1 genome orf trna

• Ribosome A and P sites revealed by length analysis of ribosome profiling data.

  PMID 25805170 · PMC4402525 · Nucleic acids research · 2015 · 7 claims · 8 setups

  Has reproduction · 81

  Accounting for variation in ribosome footprint lengths, by aligning footprints to the correct end, reveals the ribosome A and P site locations.

  escherichia saccharomyces ribosome mrna-seq hierarchical

• Searching for interpretable rules for disease mutations: a simulated annealing bump hunting strategy.

  PMID 16984653 · PMC1618409 · BMC bioinformatics · 2006 · 8 claims · 6 setups

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  The proposed feature set outperforms existing published feature sets for predicting effects of amino acid substitutions

  coli bacteriophage lac proteins svm simulated pearson

• A focused antibody library for selecting scFvs expressed at high levels in the cytoplasm.

  PMID 18034894 · PMC2241821 · BMC biotechnology · 2007 · 7 claims · 7 setups

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  A human scFv library was built on the single scFv13R4 framework with CDR3 loops diversified to mimic natural human CDR3 amino-acid distributions.

  coli hela filamentous scfv gfp sds-page fluorescence

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

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

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  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

• The commonly-used DNA probe for diffusely-adherent Escherichia coli cross-reacts with a subset of enteroaggregative E. coli.

  PMID 20025771 · PMC2803494 · BMC microbiology · 2009 · 7 claims · 5 setups

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  The daaC probe cross-hybridizes with a specific subset of EAEC strains, namely those carrying the aafA gene (AAF/II fimbriae)

  coli hep-2 pslm862 eaec colony hep-2 pcr

• Interspecies diversity of the occludin sequence: cDNA cloning of human, mouse, dog, and rat-kangaroo homologues.

  PMID 8601611 · PMC2120780 · The Journal of cell biology · 1996 · 8 claims · 7 setups

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  Full-length cDNAs encoding occludin were cloned and sequenced from rat-kangaroo (potoroo), human, mouse, and dog

  ptk2 t84 escherichia computational expression immunofluorescence immunoblotting

• Evolution of variants of yeast site-specific recombinase Flp that utilize native genomic sequences as recombination target sites.

  PMID 17003057 · PMC1635253 · Nucleic acids research · 2006 · 8 claims · 8 setups

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  Stepwise directed evolution using chimeric FLRT (FRT/genomic hybrid) intermediate sites can generate Flp variants capable of recombining native genomic FRT-like sequences from the human IL10 gene (FL-IL10A, FL-IL10B).

  coli flp il10 flp-holliday recombination site-specific computational

• Protein co-evolution, co-adaptation and interactions.

  PMID 18818697 · PMC2556093 · The EMBO journal · 2008 · 8 claims · 6 setups

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  The mirrortree method predicts protein-protein interactions by detecting pairs of protein families with similar phylogenetic trees (quantified as Pearson correlation of sequence similarity matrices).

  nuoe intra-protein coli interacting phylogenetic correlated domain-restricted

• Polymorphism and epitope sharing between the alleles of merozoite surface protein-1 of Plasmodium falciparum among Indian isolates.

  PMID 17659072 · PMC1950510 · Malaria journal · 2007 · 7 claims · 6 setups

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  PfMAD20 is the predominant PfMSP-1 allelic type among Indian field isolates

  falciparum escherichia coli-expressed recombinant pcr recombinant sds-page

• SNAP: predict effect of non-synonymous polymorphisms on function.

  PMID 17526529 · PMC1920242 · Nucleic acids research · 2007 · 7 claims · 8 setups

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  SNAP, a neural network-based method using sequence-derived information, predicts whether a non-synonymous SNP is neutral or non-neutral for protein function

  combined escherichia bacteriophage hiv-1 neural benchmark comparative

• Comparative genomics and understanding of microbial biology.

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

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  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

• Preponderance of the oncogenic V599E and V599K mutations in B-raf kinase domain is enhanced in melanoma cutaneous/subcutaneous metastases.

  PMID 15935100 · PMC1164406 · BMC cancer · 2005 · 8 claims · 4 setups

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  B-raf exon 15 somatic mutations occur in 24/60 (40%) of cutaneous/subcutaneous melanoma metastases, similar to the frequency in primary melanomas

  paraffin-embedded cloned same predicted pcr cloning blastx

• Molecular cloning and characterisation of the RESA gene, a marker of genetic diversity of Plasmodium falciparum.

  PMID 19816792 · PMC2900597 · Molecular biology reports · 2010 · 8 claims · 8 setups

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  RESA was cloned from a P. falciparum Dd2 expression library screened with human immune sera, yielding a 1,336 bp insert with a 936 bp ORF encoding a 317-aa protein.

  falciparum falciparum-infected coli sera cdna sequencing pcr

• Disturbed interaction of p21-rac with mutated p67-phox causes chronic granulomatous disease.

  PMID 8879195 · PMC2192830 · The Journal of experimental medicine · 1996 · 6 claims · 8 setups

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  The patient is a compound heterozygote for a p67-phox gene mutation: an in-frame deletion of lysine 58 on one allele and an 11-13 kb genomic deletion on the other allele.

  granulocytes granulocyte mononuclear leukocyte nbt cell-free western

• Genomewide pattern of synonymous nucleotide substitution in two complete genomes of Mycobacterium tuberculosis.

  PMID 12453367 · PMC2738538 · Emerging infectious diseases · 2002 · 8 claims · 6 setups

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  Genomewide comparison of two complete M. tuberculosis genomes reveals substantially more nucleotide diversity than prior studies based on few loci suggested

  tuberculosis putative orthologous genomewide blastp clustal nei-gojobori

• Zinc finger nucleases: custom-designed molecular scissors for genome engineering of plant and mammalian cells.

  PMID 16251401 · PMC1270952 · Nucleic acids research · 2005 · 8 claims · 8 setups

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  ZFNs combining the FokI nuclease domain with custom zinc finger proteins can deliver site-specific double-strand breaks to plant and mammalian genomes.

  foki zif268-derived coli zfns limited foot-printing x-ray

• Genetic microheterogeneity and phenotypic variation of Helicobacter pylori arginase in clinical isolates.

  PMID 17408487 · PMC1853099 · BMC microbiology · 2007 · 8 claims · 8 setups

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  Arginase activity varies more than 100-fold among H. pylori clinical isolates and laboratory-adapted strains

  minimally-passaged pylori coli arginase urease heterologous

• ksgA mutations confer resistance to kasugamycin in Neisseria gonorrhoeae.

  PMID 19097863 · PMC2723803 · International journal of antimicrobial agents · 2009 · 8 claims · 6 setups

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  Spontaneous KSG-resistant N. gonorrhoeae mutants arise exclusively through mutations in ksgA, not rpsI

  clinical gonorrhoeae coli mic spontaneous pcr