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).

• Identifying and classifying trait linked polymorphisms in non-reference species by walking coloured de bruijn graphs.

  PMID 23536903 · PMC3607606 · PloS one · 2013 · 8 claims · 9 setups

  Has reproduction · 45

  Bubbleparse detects sequence variants directly from NGS reads without a reference genome, using the coloured de Bruijn graph implementation of Cortex plus a new depth-first bubble-finding module.

  arabidopsis bubbleparse escherichia col-0 reference-free alignment-based sequence

• Characterization of a natural mutator variant of human DNA polymerase lambda which promotes chromosomal instability by compromising NHEJ.

  PMID 19806195 · PMC2751832 · PloS one · 2009 · 8 claims · 8 setups

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  The W438 hPolλ variant has reduced base substitution fidelity in vitro compared to wild-type R438

  normal recombinant hpolλ short pcr-sscp ber m13mp2

• Nucleosome formation with the testis-specific histone H3 variant, H3t, by human nucleosome assembly proteins in vitro.

  PMID 18281699 · PMC2367731 · Nucleic acids research · 2008 · 8 claims · 7 setups

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  H3t/H4 forms nucleosomes with H2A/H2B via the salt-dialysis method, similar to conventional H3.1/H4

  recombinant reconstituted his6-tagged hnap1 salt-dialysis micrococcal chaperone-mediated

• PCR-free method detects high frequency of genomic instability in prostate cancer.

  PMID 19797393 · PMC2794161 · Nucleic acids research · 2009 · 7 claims · 6 setups

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  A novel PCR-free random cloning/sequencing method can detect genomic variants that PCR-based approaches miss in heterogeneous tumor genomes.

  blood normal prostate matched pcr-free degenerate-pcr blastn

• 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

• 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

• Lightweight genome viewer: portable software for browsing genomics data in its chromosomal context.

  PMID 17877794 · PMC2238324 · BMC bioinformatics · 2007 · 7 claims · 7 setups

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  lwgv provides a lightweight alternative to large genome browsers for visualizing biological annotations and dynamic analyses without requiring a database or complex software infrastructure

  chromosome user-submitted hannon-elledge gene linkage rnai shrna

• 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

• Multiple functions of precursor BDNF to CNS neurons: negative regulation of neurite growth, spine formation and cell survival.

  PMID 19674479 · PMC2743674 · Molecular brain · 2009 · 7 claims · 8 setups

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  R125M, R127L, and R125M/R127L BDNF SNP variants are poorly cleaved, resulting in predominant secretion of proBDNF (CR-proBDNF)

  bdnf hippocampal cortical cerebellar bioinformatic western immunoprecipitation