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).

• Lift&Add-rapid and robust addition of new species to alignments of conserved non-coding sequences.

  PMID 42203687 · PMC13224966 · Bioinformatics (Oxford, England) · 2026 · 7 claims · 5 setups

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  Lift&Add, a Snakemake/bash workflow combining UCSC liftOver, Liftoff, and MAFFT, enables rapid addition of new genome sequences to existing multi-species alignments of conserved elements without requiring new whole-genome alignments.

  mm10 opossum newly vertebrate phastcons ucsc liftoff

• Adaptive history of single copy genes highly expressed in the term human placenta.

  PMID 18848617 · PMC2759754 · Genomics · 2009 · 8 claims · 6 setups

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  222 single copy eutherian genes are highly expressed (>=3x median) in the term human placenta

  term single same lists microarray comparative site

• Using several pair-wise informant sequences for de novo prediction of alternatively spliced transcripts.

  PMID 16925842 · PMC1810557 · Genome biology · 2006 · 8 claims · 4 setups

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  MARS, an extension of the Twinscan algorithm, uses multiple pairwise informant genomes to predict human alternatively spliced transcripts de novo without expressed sequence information.

  genome tissues novo pairwise rt-pcr

• Comparative genomics of Lbx loci reveals conservation of identical Lbx ohnologs in bony vertebrates.

  PMID 18541024 · PMC2446394 · BMC evolutionary biology · 2008 · 8 claims · 3 setups

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  Extant bony vertebrates (osteichthyans) retain only Lbx1- and Lbx2-type genes; no distinct Lbx3/Lbx4 proteins exist.

  osteichthyan aligned genome blast maximum comparative

• Sequence occurrence and structural uniqueness of a G-quadruplex in the human c-kit promoter.

  PMID 17720713 · PMC2034477 · Nucleic acids research · 2007 · 8 claims · 4 setups

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  The native 22-nt c-kit87 sequence occurs only once in the entire human genome.

  genome synthetic c-kit87 c-kit genome-wide circular molecular

• Ensembl 2007.

  PMID 17148474 · PMC1761443 · Nucleic acids research · 2007 · 8 claims · 7 setups

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  Ensembl added 18 new chordate genomes this year, increasing total genomes available from 15 to 33, the largest yearly increase to date.

  low-coverage cow chicken genome genome standard customized

• How accurately is ncRNA aligned within whole-genome multiple alignments?

  PMID 17963514 · PMC2206062 · BMC bioinformatics · 2007 · 7 claims · 4 setups

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  MULTIZ does a fairly accurate job of aligning ncRNA regions across 17 vertebrate genomes, but better alignments exist in some regions.

  genome vertebrate nonhuman genomic sequence whole-genome covariance