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).
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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
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
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Has reproduction · 67
Assembly of Macromolecular Complexes in the Whole-Cell Model of a Minimal Cell.
PMID 41427637 · PMC12794154 · The journal of physical chemistry. B · 2026 · 8 claims · 6 setups
Assembly pathways for 21 unique macromolecular complexes (RNAP, ribosome, degradosome, ATP synthase, ABC transporters, etc.) were incorporated into the existing Syn3A whole-cell model
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Has reproduction · 68
Genome-wide DNA hypermethylation opposes healing in patients with chronic wounds by impairing epithelial-mesenchymal transition.
PMID 35819852 · PMC9433101 · The Journal of clinical investigation · 2022 · 8 claims · 8 setups
Chronic wound-edge tissue shows genome-wide DNA hypermethylation compared with unwounded skin
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The genomics of probiotic intestinal microorganisms.
PMID 15998456 · PMC1175979 · Genome biology · 2005 · 8 claims · 8 setups
Genomic characterization of probiotic and commensal intestinal bacteria will deepen understanding of their beneficial effects on host health
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Functional genomics in zebrafish permits rapid characterization of novel platelet membrane proteins.
PMID 19109564 · PMC2680375 · Blood · 2009 · 8 claims · 6 setups
Zebrafish morpholino knockdown combined with a laser-induced arterial thrombosis assay is a fast, powerful method for initial functional screening of novel platelet genes.
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TB database: an integrated platform for tuberculosis research.
PMID 18835847 · PMC2686437 · Nucleic acids research · 2009 · 8 claims · 8 setups
TBDB is an integrated database providing access to TB genomic data and resources relevant to discovery/development of TB drugs, vaccines and biomarkers.
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Molecular helminthology in the Rockies. Keystone Symposium on Molecular Helminthology, Copper Mountain, Colorado, USA, 9-13 April 2005.
PMID 15998458 · PMC1175981 · Genome biology · 2005 · 8 claims · 8 setups
The Schistosoma mansoni genome (~300 Mb) is nearing completion via whole-genome shotgun sequencing at ninefold coverage, with an estimated 15,000-20,000 protein-coding genes
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Has reproduction · 71
A method for selectively enriching microbial DNA from contaminating vertebrate host DNA.
PMID 24204593 · PMC3810253 · PloS one · 2013 · 8 claims · 7 setups
MBD-Fc bound to Protein A paramagnetic beads selectively binds methylated (vertebrate host) DNA, depleting it from mixed samples
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Has reproduction · 88
Chromosome-Scale Assembly of the Complete Genome Sequence of Porcisia hertigi, Isolate C119, Strain LV43.
PMID 34647802 · PMC8515887 · Microbiology resource announcements · 2021 · 6 claims · 8 setups
The complete, chromosome-scale genome sequence of Porcisia hertigi (isolate C119, strain LV43) was assembled using combined short- and long-read sequencing technologies.
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Has reproduction · 78
Chromosome-Scale Assembly of the Complete Genome Sequence of Leishmania (Mundinia) orientalis, Isolate LSCM4, Strain LV768.
PMID 34498920 · PMC8428255 · Microbiology resource announcements · 2021 · 6 claims · 8 setups
The complete genome sequence of Leishmania (Mundinia) orientalis, isolate LSCM4, strain LV768, was determined using combined short-read and long-read sequencing.
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Has reproduction · 67
Evidence for L1-associated DNA rearrangements and negligible L1 retrotransposition in glioblastoma multiforme.
PMID 27843499 · PMC5105311 · Mobile DNA · 2016 · 6 claims · 7 setups
Canonical (endonuclease-dependent, TPRT-driven) L1 retrotransposition is absent or negligible in GBM tumours and cultured GBM cell lines
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Has reproduction · 100
Analysis of the Taxonomy, Synteny, and Virulence Factors for Soft Rot Pathogen Pectobacterium aroidearum in Amorphophallus konjac Using Comparative Genomics.
PMID 35910650 · PMC9326479 · Frontiers in microbiology · 2022 · 8 claims · 8 setups
The causal agent of konjac soft rot in China is Pectobacterium aroidearum, confirmed via in vitro/in vivo pathogenicity tests, ANI, dDDH, and phylogenomic analysis.
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NeMeSys: a biological resource for narrowing the gap between sequence and function in the human pathogen Neisseria meningitidis.
PMID 19818133 · PMC2784325 · Genome biology · 2009 · 8 claims · 5 setups
Determined and manually annotated the complete genome sequence of N. meningitidis clinical isolate strain 8013
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Integrating complex genomic datasets and tumour cell sensitivity profiles to address a 'simple' question: which patients should get this drug?
PMID 20003409 · PMC2799438 · BMC medicine · 2009 · 8 claims · 5 setups
A panel of 48 genomically characterized breast cancer cell lines can model patient tumour heterogeneity to identify biomarkers predicting response to PG-11047
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Malaria genomics meets drug-resistance phenotyping in the field.
PMID 19664295 · PMC2745762 · Genome biology · 2009 · 8 claims · 8 setups
Significantly longer parasite clearance times in Pailin (western Cambodia) versus Wang Pha (Thailand-Myanmar border) establish the presence of artemisinin resistance in western Cambodia.
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A comparison of programmed cell death between species.
PMID 11178240 · PMC138857 · Genome biology · 2000 · 8 claims · 8 setups
The core apoptotic pathway (CED-3/caspases, CED-4/Apaf-1, CED-9/Bcl-2, EGL-1) is conserved across C. elegans, Drosophila, and mammals.
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Better smelling through genetics: mammalian odor perception.
PMID 18938244 · PMC2590501 · Current opinion in neurobiology · 2008 · 8 claims · 8 setups
Odorant receptor (OR) gene repertoire size and pseudogene fraction vary dramatically across mammalian species
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Has reproduction · 74
Transcriptome profiling of Giardia intestinalis using strand-specific RNA-seq.
PMID 23555231 · PMC3610916 · PLoS computational biology · 2013 · 8 claims · 8 setups
Most of the G. intestinalis genome is transcribed in in vitro-grown trophozoites, but at vastly different expression levels.