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).

• Evolution of insect proteomes: insights into synapse organization and synaptic vesicle life cycle.

  PMID 18257909 · PMC2374702 · Genome biology · 2008 · 8 claims · 3 setups

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  Compiled a list of 120 core presynaptic gene prototypes (PS120) and catalogued their conservation across insect proteomes.

  insect vamp2 ps120 comparative sequence protein-protein

• Comparative Genome Analysis of 16SrXII-A 'Candidatus Phytoplasma solani' POT Transmitted by Hyalesthes obsoletus.

  PMID 41597744 · PMC12843639 · Microorganisms · 2026 · 7 claims · 8 setups

  Has reproduction · 95

  The complete 832,614 bp circular chromosome of the H. obsoletus-transmissible 'Ca. P. solani' 16SrXII-A strain POT was assembled and functionally reconstructed.

  catharanthus pacbio smrt pot experimental endpoint smrt

• Multiple whole genome alignments and novel biomedical applications at the VISTA portal.

  PMID 17488840 · PMC1933192 · Nucleic acids research · 2007 · 8 claims · 4 setups

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  A novel multiple whole-genome alignment algorithm treats all genomes symmetrically, avoiding dependence on a single base/reference genome

  genome vertebrate multi-species whole-genome conservation non-synonymous

• Retroposition and evolution of the DNA-binding motifs of YY1, YY2 and REX1.

  PMID 17478514 · PMC1904287 · Nucleic acids research · 2007 · 8 claims · 5 setups

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  62 YY1-related sequences were identified across genomes ranging from flying insects to humans, with high zinc finger domain conservation

  genome insect yy1-related zinc blast sequence synonymous

• The UCSC Genome Browser Database: update 2006.

  PMID 16381938 · PMC1347506 · Nucleic acids research · 2006 · 8 claims · 8 setups

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  The UCSC Genome Browser Database (GBD) provides integrated sequence and annotation data, with web tools (Genome Browser, Table Browser, Proteome Browser, Gene Sorter, BLAT, In Silico PCR) for visualizing and querying genomes of about a dozen vertebrate species and several model organisms.

  dog vertebrate encode genome comparative automated cross-species

• U7 snRNAs: a computational survey.

  PMID 18267300 · PMC5054213 · Genomics, proteomics & bioinformatics · 2007 · 8 claims · 6 setups

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  A computational (BLAST-based) survey identified bona fide U7 snRNA genes with characteristic upstream promoter elements (PSE) across most vertebrate genomes examined, plus numerous pseudogenes.

  mammalian drosophilid aligned basal blast sequence consensus

• CONTRAST: a discriminative, phylogeny-free approach to multiple informant de novo gene prediction.

  PMID 18096039 · PMC2246271 · Genome biology · 2007 · 8 claims · 5 setups

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  CONTRAST predicts exact coding region structures for 65% more human genes than the previous state-of-the-art de novo predictor (N-SCAN)

  genome sequence drosophila novo gene coding

• Ensembl 2005.

  PMID 15608235 · PMC540092 · Nucleic acids research · 2005 · 8 claims · 4 setups

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  Ensembl's automatic gene build system can flexibly and reliably annotate a wide variety of genomes with limited species-specific evidence.

  chicken genomes vertebrate annotated experimental gene pairwise

• SilkDB v2.0: a platform for silkworm (Bombyx mori ) genome biology.

  PMID 19793867 · PMC2808975 · Nucleic acids research · 2010 · 8 claims · 8 setups

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  A new 8.5x-coverage silkworm genome assembly with N50 scaffold size of ~3.7 Mb over a 432 Mb genome represents a significant quality improvement over the prior draft.

  bombyx whole-genome snp novo