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).

• 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

• 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

• Forward genetic analysis of the apicomplexan cell division cycle in Toxoplasma gondii.

  PMID 18282098 · PMC2242837 · PLoS pathogens · 2008 · 8 claims · 6 setups

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  A high-throughput ENU mutagenesis screen isolated 165 temperature-sensitive (ts) Toxoplasma growth mutants from ~60,000 clones.

  gondii genomic chemical flow immunofluorescence

• 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

• 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

• 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

• Coxiella burnetii genotyping.

  PMID 16102309 · PMC3320512 · Emerging infectious diseases · 2005 · 8 claims · 5 setups

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  Multispacer sequence typing (MST) is the first reliable method for typing Coxiella burnetii isolates

  coxiella burnetii matrix sequence pcr molecular pcr-based

• 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

• 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

• Variation in the E2-binding domain of HPV 16 is associated with high-grade squamous intraepithelial lesions of the cervix.

  PMID 11308254 · PMC2363853 · British journal of cancer · 2001 · 8 claims · 6 setups

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  E2 gene disruption in the analysed regions is significantly more frequent in high-grade SILs than low-grade SILs

  paraffin-embedded hpv16-positive representative cervical pcr restriction bidirectional

• A genome annotation-driven approach to cloning the human ORFeome.

  PMID 15461802 · PMC545604 · Genome biology · 2004 · 8 claims · 8 setups

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  Existing human cDNA clone collections together provide only 60% coverage of full-length chromosome 22 ORFs, with the best single collection (MGC) providing 48%

  chromosome pooled t-tailed naga comparative rt-pcr sanger

• 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

• Mycoplasma genitalium: an efficient strategy to generate genetic variation from a minimal genome.

  PMID 17784912 · PMC2169797 · Molecular microbiology · 2007 · 8 claims · 6 setups

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  MG192 is highly variable among and within M. genitalium strains both in vitro and in vivo

  genitalium clinical urine pairwise pcr serial

• Genetic diversity of clinical isolates of Bacillus cereus using multilocus sequence typing.

  PMID 18990211 · PMC2585095 · BMC microbiology · 2008 · 8 claims · 7 setups

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  The 55 clinical B. cereus isolates were phylogenetically diverse, comprising 38 sequence types (STs) distributed across two of three previously described clades.

  clinical concatenated cereus isolates multilocus phylogenetic pcr

• 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

• Development of lead hammerhead ribozyme candidates against human rod opsin mRNA for retinal degeneration therapy.

  PMID 19094986 · PMC3388947 · Experimental eye research · 2009 · 8 claims · 3 setups

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  Three lead hhRz candidates (CUC↓266, CUC↓1411, AUA↓1414) significantly knock down human RHO protein expression relative to control (p<0.05)

  rho expression secondary western dicistronic

• 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

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  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

• Leveraging human genomic information to identify nonhuman primate sequences for expression array development.

  PMID 16288651 · PMC1314899 · BMC genomics · 2005 · 8 claims · 6 setups

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  Human genomic DNA sequence can be leveraged to obtain 3' end sequence of NHP orthologs, which can then be used to generate NHP oligonucleotide microarrays

  refseq macaca genomic rhesus exon pcr molecular

• Use of modified U1 snRNAs to inhibit HIV-1 replication.

  PMID 17158512 · PMC1802557 · Nucleic acids research · 2007 · 7 claims · 6 setups

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  U1 snRNAs complementary to 5 of 15 targeted conserved regions in the HIV-1 terminal exon significantly suppress HIV-1 protein expression and viral replication, coincident with loss of viral RNA

  hiv-1 293t hela bioinformatic western reporter

• Cryptic loxP sites in mammalian genomes: genome-wide distribution and relevance for the efficiency of BAC/PAC recombineering techniques.

  PMID 17284462 · PMC1865043 · Nucleic acids research · 2007 · 6 claims · 6 setups

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  Cryptic lox P sites occur frequently and are homogeneously distributed across the mouse genome (1.2 primary sites per megabase).

  genome bac coli el350 genome-wide sequence bacterial