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 6

System / cell line: whole-genome ✕ Assay: pyrosequencing ✕ Clear

Genomic diversity and evolution of Mycobacterium ulcerans revealed by next-generation sequencing.

PMID 19806175 · PMC2736377 · PLoS pathogens · 2009 · 8 claims · 6 setups

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Genome sequencing of three M. ulcerans strains (NM20/02, NM31/04, Jp8756) identified thousands of SNPs relative to reference strain Agy99

ulcerans collection snp whole-genome comparative read
Massively parallel pyrosequencing in HIV research.

PMID 18614863 · PMC4221253 · AIDS (London, England) · 2008 · 8 claims · 8 setups

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Massively parallel pyrosequencing platforms (454/Roche, Solexa/Illumina) enable very high-throughput DNA sequencing, up to ~1 billion bases per run

mammoth hiv hiv-infected honey pyrosequencing pcr 16s
Short-term genome evolution of Listeria monocytogenes in a non-controlled environment.

PMID 19014550 · PMC2642827 · BMC genomics · 2008 · 6 claims · 6 setups

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The 2000 listeriosis outbreak was likely caused by an L. monocytogenes strain that persisted in the food processing facility for at least 12 years since 1988

monocytogenes additional food j774 whole-genome comparative pcr
High throughput sequencing and proteomics to identify immunogenic proteins of a new pathogen: the dirty genome approach.

PMID 20037647 · PMC2793016 · PloS one · 2009 · 7 claims · 7 setups

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A dirty genome approach using unfinished, unclosed genome sequences combined with proteomics can rapidly identify immunogenic proteins useful for diagnostic tool development

parachlamydia spots coli recombinant pyrosequencing solexa gel
Population differentiation and epidemic tracking of Bursaphelenchus xylophilus in China based on chromosome-level assembly and whole-genome sequencing data.

PMID 34839581 · PMC9300093 · Pest management science · 2022 · 6 claims · 8 setups

Has reproduction · 44

Generated the first chromosome-level genome assembly (AH1) of B. xylophilus using PacBio, Illumina, BioNano, and Hi-C data

xylophilus snp smrt short-read bionano
Array-based profiling of reference-independent methylation status (aPRIMES) identifies frequent promoter methylation and consecutive downregulation of ZIC2 in pediatric medulloblastoma.

PMID 17344319 · PMC1874664 · Nucleic acids research · 2007 · 7 claims · 7 setups

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aPRIMES is a novel array-based method that detects direct (absolute) methylation status of CGIs via competitive hybridization of McrBC-digested (methylated) versus HpaII/BstUI-digested (unmethylated) DNA from the same genome, avoiding reference-tissue and copy-number biases

pediatric tumor eight desmoplastic aprimes bisulfite quantitative

Experiments

Genomic diversity and evolution of Mycobacterium ulcerans revealed by next-generation sequencing.

Massively parallel pyrosequencing in HIV research.

Short-term genome evolution of Listeria monocytogenes in a non-controlled environment.

High throughput sequencing and proteomics to identify immunogenic proteins of a new pathogen: the dirty genome approach.

Population differentiation and epidemic tracking of Bursaphelenchus xylophilus in China based on chromosome-level assembly and whole-genome sequencing data.

Array-based profiling of reference-independent methylation status (aPRIMES) identifies frequent promoter methylation and consecutive downregulation of ZIC2 in pediatric medulloblastoma.