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).

• Applications for protein sequence-function evolution data: mRNA/protein expression analysis and coding SNP scoring tools.

  PMID 16912992 · PMC1538848 · Nucleic acids research · 2006 · 7 claims · 8 setups

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  PANTHER HMMs built from family/subfamily multiple sequence alignments can classify novel protein sequences into functional groups based on statistically significant HMM match scores

  input gene genome-wide genes sequence gene numerical

• Transcriptional landscape of repetitive elements in normal and cancer human cells.

  PMID 25012247 · PMC4122776 · BMC genomics · 2014 · 8 claims · 8 setups

  Has reproduction · 76

  RepEnrich, a computational method that uses all mapping reads (uniquely mapping plus multi-mapping reads assigned to repetitive element subfamily assemblies/pseudogenomes), quantifies genome-wide repetitive element enrichment

  chromosomes lines imr-90 prostate simulated pol chip-seq

• TEPEAK: A novel method for identifying and characterizing polymorphic transposable elements in non-model species populations.

  PMID 41494038 · PMC12788660 · PLoS computational biology · 2026 · 8 claims · 6 setups

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  TEPEAK identifies and characterizes polymorphic TEs in populations without any prior TE sequence or loci information, using only a chromosome-level reference assembly.

  horse pooled sequences consensus whole-genome insertion hierarchical