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).

• Evolutionary history of the UCP gene family: gene duplication and selection.

  PMID 18980678 · PMC2584656 · BMC evolutionary biology · 2008 · 8 claims · 8 setups

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  The UCP gene family arose through two ancestral gene duplications early in vertebrate evolution, producing the UCP1, UCP2 and UCP3 lineages.

  vertebrate ucp human-mouse ucp1 sequence phylogenetic gene

• Protein coding potential of retroviruses and other transposable elements in vertebrate genomes.

  PMID 15716312 · PMC549403 · Nucleic acids research · 2005 · 8 claims · 5 setups

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  About 1000 genes across four vertebrate gene sets analyzed contain at least one RETRA marker protein domain

  predicted non-masked genome interpro hmm tblastn inter-species

• Mining the draft human genome.

  PMID 11236999 · PMC2658632 · Nature · 2001 · 8 claims · 7 setups

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  Protein-coding exons account for only about 3% of the human genome DNA, with repeat sequences making up around 46%.

  genome unfinished drosophila tetraodon psi-blast domain sequence

• Adapting to a changing world: RAG genomics and evolution.

  PMID 16004728 · PMC3525258 · Human genomics · 2005 · 8 claims · 7 setups

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  RAG-1/RAG-2 origin is a foundational hallmark of adaptive immunity, enabling V(D)J recombination of antigen receptor genes.

  rag-1 patients zebrafish vertebrate comparative site-directed clinical

• Molecular evolution of Cide family proteins: novel domain formation in early vertebrates and the subsequent divergence.

  PMID 18500987 · PMC2426694 · BMC evolutionary biology · 2008 · 8 claims · 5 setups

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  Sequences homologous to the CIDE-N domain/NCD show a wide phylogenetic distribution, from hydra and sea anemone to mammals, while true Cide proteins are restricted to vertebrates.

  organisms cide cideb hmmer tblastn sequence

• Empirical codon substitution matrix.

  PMID 15927081 · PMC1173088 · BMC bioinformatics · 2005 · 8 claims · 5 setups

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  The authors present the first empirical codon substitution matrix built entirely from alignments of vertebrate coding DNA sequences.

  orthologous million codon same pairwise empirical comparative

• Evola: Ortholog database of all human genes in H-InvDB with manual curation of phylogenetic trees.

  PMID 17982176 · PMC2238928 · Nucleic acids research · 2008 · 6 claims · 7 setups

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  Evola combines genome synteny-based computational ortholog detection with manual curation of phylogenetic trees by experts to yield more reliable orthologs than automated pairwise methods

  genome h-invdb gene sets genome transcript-to-genome coding

• Comparative genomics.

  PMID 14624258 · PMC261895 · PLoS biology · 2003 · 8 claims · 7 setups

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  Conserved DNA between species tends to encode shared functional features, while divergent DNA underlies species differences

  caenorhabditis yeast mammalian vertebrate whole-genome comparative interspecies-similarity-informed

• Dcode.org anthology of comparative genomic tools.

  PMID 15980535 · PMC1160116 · Nucleic acids research · 2005 · 8 claims · 7 setups

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  The dcode.org suite (zPicture, Mulan, eShadow, rVista 2.0, multiTF, Creme 2.0, ECR Browser) provides integrated tools for comparative genomic analysis and non-coding regulatory element discovery.

  dlx1 hoxa prothrombin gene comparative multi-species phylogenetic

• Bioinformatic mapping of AlkB homology domains in viruses.

  PMID 15627404 · PMC544882 · BMC genomics · 2005 · 8 claims · 8 setups

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  AlkB-like domains are found in at least 22 different single-stranded RNA positive-strand plant viruses, mainly within a subgroup of the Flexiviridae family.

  ncbi 146-sequence representative hel psi-blast pfam profile

• 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

• Of rats and men.

  PMID 15003114 · PMC395761 · Genome biology · 2004 · 8 claims · 10 setups

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  The rat genome has been sequenced to draft level, with over 90% of the genome sampled using more than 36 million sequence reads (assembly version 3.1)

  rattus cftr fugu transgenic whole-genome comparative genome