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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Genomic and bioinformatics analysis of human adenovirus type 37: new insights into corneal tropism.
PMID 18471294 · PMC2397415 · BMC genomics · 2008 · 7 claims · 7 setups
The complete genome of HAdV-37 was sequenced and annotated (35,213 bp, 56.6% GC content, 35 predicted coding sequences plus 8 hypothetical ORFs)
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Patterns and rates of intron divergence between humans and chimpanzees.
PMID 17309804 · PMC1852421 · Genome biology · 2007 · 8 claims · 6 setups
Intron divergence (Ki) is strongly positively correlated with intron length
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Has reproduction · 72
Analysis of the genome of the New Zealand giant collembolan (Holacanthella duospinosa) sheds light on hexapod evolution.
PMID 29041914 · PMC5644144 · BMC genomics · 2017 · 8 claims · 8 setups
Phylogenomic analysis (370,877 amino acids) placed H. duospinosa within the family Neanuridae
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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 · 93
Firefly genomes illuminate parallel origins of bioluminescence in beetles.
PMID 30324905 · PMC6191289 · eLife · 2018 · 7 claims · 8 setups
Bioluminescence arose independently (parallel/convergent origins) in fireflies and click beetles rather than from a single common ancestral origin.
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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 exhibits genome-wide DNA hypermethylation, with hypermethylation more prominent than hypomethylation across differentially methylated regions.
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Whole genome comparative studies between chicken and turkey and their implications for avian genome evolution.
PMID 18410676 · PMC2375447 · BMC genomics · 2008 · 8 claims · 7 setups
Chicken and turkey genomes differ by only two inter-chromosomal rearrangements (GGA2 orthologous to MGA3+6; GGA4 orthologous to MGA4+9), both involving centromeres.
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Has reproduction · 99
Systematic benchmarking of tools for CpG methylation detection from nanopore sequencing.
PMID 34103501 · PMC8187371 · Nature communications · 2021 · 8 claims · 6 setups
Existing Nanopore methylation detection tools present a tradeoff between false positives and false negatives and show high dispersion relative to expected methylation frequency values.
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Has reproduction
Methylation patterns of the nasal epigenome of hospitalized SARS-CoV-2 positive patients reveal insights into molecular mechanisms of COVID-19.
PMID 40170038 · PMC11963311 · BMC medical genomics · 2025 · 7 claims · 7 setups
Differential DNA methylation occurs predominantly in intergenic regions and low methylated regions (LMRs), highlighting the role of distal regulatory elements in COVID-19 severity.
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CoMoDis: composite motif discovery in mammalian genomes.
PMID 17130158 · PMC1702496 · Nucleic acids research · 2007 · 7 claims · 4 setups
CoMoDis is a new bioinformatics tool that streamlines computational identification of novel regulatory modules starting from a single seed motif
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Bases and spaces: resources on the web for accessing the draft human genome.
PMID 11178254 · PMC138875 · Genome biology · 2000 · 8 claims · 8 setups
By combining currently available genomic databases and mapping resources (GenBank/Entrez, UniGene, RH maps, BAC fingerprint maps, Ensembl, NIX), it is possible to devise strategies that fully exploit the fragmentary draft human genome sequence.
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Has reproduction · 80
Structure of the intergenic spacers in chicken ribosomal DNA.
PMID 31655542 · PMC6815422 · Genetics, selection, evolution : GSE · 2019 · 8 claims · 6 setups
Long-read PacBio RSII sequencing of a BAC clone plus HGAP assembly can resolve the complete, highly repetitive chicken IGS structure that short-read (Illumina) sequencing previously failed to assemble.
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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
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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Speeding disease gene discovery by sequence based candidate prioritization.
PMID 15766383 · PMC1274252 · BMC bioinformatics · 2005 · 7 claims · 8 setups
Disease genes (OMIM) differ significantly from non-disease genes in sequence-based features including gene/cDNA/protein size, exon number, homolog conservation, secretion signal, 3' UTR length, CpG islands, and distance to nearest gene.