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).

• Plasmid transmission dynamics and evolution of partner quality in a natural population of Rhizobium leguminosarum.

  PMID 41212030 · PMC12691615 · mBio · 2025 · 8 claims · 8 setups

  Has reproduction · 86

  Of the four most frequent plasmid types, types II and III have more stable size, larger core genomes, and track the chromosomal phylogeny (more vertical transmission), while types I and IV (pSym) vary in size and gene content with phylogenies consistent with frequent horizontal transmission.

  clover-associated plasmids plasmidome replicons long-read k-mer genome

• Detecting DNA modifications from SMRT sequencing data by modeling sequence context dependence of polymerase kinetic.

  PMID 23516341 · PMC3597545 · PLoS computational biology · 2013 · 8 claims · 7 setups

  Has reproduction · 44

  Local sequence context strongly determines position-specific polymerase kinetic rate: roughly 80% of IPD variation is explained by a 10 bp context (7 bases upstream, 2 bases downstream of the incorporation site), saturating at 7 bases upstream.

  plasmid coli wild-type artificial smrt read-mixing distributional

• Description of a PCR-based technique for DNA splicing and mutagenesis by producing 5' overhangs with run through stop DNA synthesis utilizing Ara-C.

  PMID 16137330 · PMC1208860 · BMC biotechnology · 2005 · 7 claims · 7 setups

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  Two adjacent Ara-C molecules incorporated into a PCR primer produce mild template-dependent polymerization termination, generating 5' overhangs usable for cohesive-end ligation.

  plasmid pcr gel-isolated ligated pcr gel ligation

• Headloop suppression PCR and its application to selective amplification of methylated DNA sequences.

  PMID 16091627 · PMC1184225 · Nucleic acids research · 2005 · 8 claims · 5 setups

  Full-text index only

  Headloop PCR: a 5' primer extension homologous to internal amplicon sequence causes hairpin formation after incorporation, suppressing further amplification of the matching sequence while unaffected sequences amplify normally

  plasmid genomic bacterial real-time methylation-specific

• Double-strand breaks in the myotonic dystrophy type 1 and the fragile X syndrome triplet repeat sequences induce different types of mutations in DNA flanking sequences in Escherichia coli.

  PMID 17012280 · PMC1636463 · Nucleic acids research · 2006 · 7 claims · 5 setups

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  DSBs induced at the TRS/vector junction (EcoRV site) generate numerous mutagenic events in flanking sequences, whereas DSBs within the repeat tract (EcoRI site) produce no such mutants

  coli plasmids plasmid white plasmid sequencing non-b

• Evolution of two distinct phylogenetic lineages of the emerging human pathogen Mycobacterium ulcerans.

  PMID 17900363 · PMC2098775 · BMC evolutionary biology · 2007 · 8 claims · 4 setups

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  M. ulcerans has evolved into five InDel haplotypes that separate into two distinct phylogenetic lineages: a 'classical' lineage (Africa, Australia, South East Asia) and an 'ancestral' lineage (Asia, South America, Mexico)

  ulcerans marinum plasmid-based pcr genome

• Low density DNA microarray for detection of most frequent TP53 missense point mutations.

  PMID 15713227 · PMC553977 · BMC biotechnology · 2005 · 7 claims · 6 setups

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  A double tandem hybridization microarray with 7-nt gap targets and 7-mer capture probes can search for 9 point mutations in TP53 codons 248, 249, and 273

  genomic pcr six same pcr single-stranded oligonucleotide

• DNA bar coding and pyrosequencing to identify rare HIV drug resistance mutations.

  PMID 17576693 · PMC1934997 · Nucleic acids research · 2007 · 6 claims · 7 setups

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  DNA bar coding combined with pyrosequencing allows parallel, deep characterization of drug resistance mutations across many HIV populations in a single experiment

  hiv pooled plasma pyrosequencing conventional rt-pcr

• Analysis of chimpanzee history based on genome sequence alignments.

  PMID 18421364 · PMC2278377 · PLoS genetics · 2008 · 8 claims · 6 setups

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  Bonobos and common chimpanzees separated approximately 1.29 million years ago

  bonobo bonobos chimpanzee simulated shotgun sequenom principal

• Proposed methods for testing and selecting the ERCC external RNA controls.

  PMID 16266432 · PMC1325234 · BMC genomics · 2005 · 8 claims · 5 setups

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  A consortium-developed, standardized set of external RNA control transcripts can be used to assess technical performance in gene expression assays (microarray and QRT-PCR)

  candidate linearized transcripts pools sequence transcription quality

• The use of multiple displacement amplification to amplify complex DNA libraries.

  PMID 18285362 · PMC2275127 · Nucleic acids research · 2008 · 7 claims · 8 setups

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  MDA alone cannot select against/remove plasmid ligation multimers, unlike bacterial propagation

  hes3 hes3-derived coli plasmids isolation flcdna gis-pet

• In vivo application of RNA interference: from functional genomics to therapeutics.

  PMID 16096010 · PMC7112075 · Advances in genetics · 2005 · 7 claims · 7 setups

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  RNAi operates through two mechanistically related but distinct pathways: cytoplasmic delivery of siRNA duplexes and nuclear delivery of shRNA expression cassettes that mimic miRNA

  mice tumor laser-induced herpetic cationic intraperitoneal aqueous

• New approaches to the analysis of palindromic sequences from the human genome: evolution and polymorphism of an intronic site at the NF1 locus.

  PMID 16340004 · PMC1310899 · Nucleic acids research · 2005 · 7 claims · 8 setups

  Full-text index only

  Long pure palindromes (>~200 bp) cannot be stably cloned in E.coli due to cruciform-driven instability, and no E.coli mutant fully overcomes this cloning block.

  individuals e.coli cerevisiae yeast pcr plasmid phi-29

• Engineered apoptotic nucleases for chromatin research.

  PMID 17626049 · PMC1935020 · Nucleic acids research · 2007 · 8 claims · 6 setups

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  Inserting TEVP cleavage sites immediately downstream of the two caspase-3 sites in DFF45 (I1I2 mutant) makes DFF40 nuclease activity exclusively dependent on TEVP cleavage (DFF-T)

  recombinant cerevisiae coli western plasmid serial

• A biomedically enriched collection of 7000 human ORF clones.

  PMID 18231609 · PMC2211400 · PloS one · 2008 · 8 claims · 4 setups

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  Produced and made available over 7000 fully sequence-verified plasmid ORF clones representing over 3400 unique human genes, in both closed (stop codon) and fusion (no stop codon) formats.

  genes mgc plasmid literature pcr sequence

• Benefit from decline: the primary transcriptome of Alteromonas macleodii str. Te101 during Trichodesmium demise.

  PMID 29335641 · PMC5864184 · The ISME journal · 2018 · 7 claims · 6 setups

  Has reproduction

  Increasing salinity to >=43 ppt inhibits Trichodesmium growth/increases mortality while stimulating growth of associated Alteromonas, shifting community dominance to the heterotroph

  alteromonas co-culture trichodesmium differential bulk whole-genome

• getSequenceInfo: a suite of tools allowing to get genome sequence information from public repositories.

  PMID 35804320 · PMC9264741 · BMC bioinformatics · 2022 · 8 claims · 8 setups

  Has reproduction · 99

  getSequenceInfo (gSeqI) allows programmatic (CLI) or GUI-based retrieval of sequence data and metadata from GenBank, RefSeq, and ENA across Linux, MacOS, and Windows.

  genome complete same coronavirus nuclescore resistance mlst

• A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms.

  PMID 15592405 · PMC2263125 · Nature · 2004 · 8 claims · 8 setups

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  A genetic variation map of 2.8 million SNPs was constructed for chicken by comparing 3 domestic breeds to Red Jungle Fowl

  domestic red same white partial comparative pcr

• High-precision mapping of protein protein interfaces: an integrated genetic strategy combining en masse mutagenesis and DNA-level parallel analysis on a yeast two-hybrid platform.

  PMID 17702760 · PMC2018616 · Nucleic acids research · 2007 · 7 claims · 4 setups

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  An integrated strategy combining en masse pentapeptide insertion mutagenesis, yeast two-hybrid screening, and parallel genetic footprinting can map protein-protein interfaces at amino acid precision and is generally applicable to any interacting protein pair.

  saccharomyces plasmid pooled individual yeast pcr-based restriction

• Complete genome of Phenylobacterium zucineum--a novel facultative intracellular bacterium isolated from human erythroleukemia cell line K562.

  PMID 18700039 · PMC2529317 · BMC genomics · 2008 · 8 claims · 6 setups

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  Complete genome of P. zucineum HLK1T consists of a 3,996,255 bp circular chromosome and a 382,976 bp circular plasmid encoding 3,861 proteins, 42 tRNAs, and one 16S-23S-5S rRNA operon

  phenylobacterium zucineum bacteria genome cog comparative