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).

• Structural evolution of the protein kinase-like superfamily.

  PMID 16244704 · PMC1261164 · PLoS computational biology · 2005 · 8 claims · 5 setups

  Full-text index only

  All kinases in the superfamily share a 'universal core' domain consisting only of the regions required for ATP binding and the phosphotransfer reaction.

  bank representative same kinase comparative manual structure-annotated

• An analysis of human microRNA and disease associations.

  PMID 18923704 · PMC2559869 · PloS one · 2008 · 8 claims · 8 setups

  Full-text index only

  MicroRNAs tend to show similar dysfunctional evidence (both up- or both down-regulated) for diseases within the same disease cluster, and different dysfunctional evidence between different disease clusters.

  literature-derived diseases mirnas mirna literature bipartite mirna

• Manual annotation and analysis of the defensin gene cluster in the C57BL/6J mouse reference genome.

  PMID 20003482 · PMC2807441 · BMC genomics · 2009 · 8 claims · 6 setups

  Full-text index only

  Manual annotation of the mouse Chromosome 8 defensin region identifies 98 gene loci: 54 in the alpha-defensin cluster and 44 in the beta-defensin cluster

  c57bl orthologous alpha-defensin defensin manual comparative sequence

• Ensembl 2013.

  PMID 23203987 · PMC3531136 · Nucleic acids research · 2013 · 8 claims · 8 setups

  Has reproduction · 85

  Ensembl (http://www.ensembl.org) provides genome information for sequenced chordate genomes, currently supporting 70 species with a focus on human, mouse, zebrafish and rat.

  genome species supported variants evidence-based rna-seq chip-seq

• Development of an integrated genome informatics, data management and workflow infrastructure: a toolbox for the study of complex disease genetics.

  PMID 15601538 · PMC3525068 · Human genomics · 2004 · 8 claims · 8 setups

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  An integrated system combining Ensembl, ACeDB, Gbrowse and custom relational databases provides a scalable genome informatics and workflow infrastructure for complex disease gene discovery.

  pcr candidate embl clinical snp manual homology

• Identifying related L1 retrotransposons by analyzing 3' transduced sequences.

  PMID 12734010 · PMC156586 · Genome biology · 2003 · 8 claims · 6 setups

  Full-text index only

  L1 elements with transduction-derived 3' sequence (L1-TDs) can be computationally identified using RepeatMasker/TSDfinder and grouped into families sharing a common progenitor via BLAST comparison of downstream sequences.

  genome database l1-td ncbi genome-wide blast pairwise

• The DNA sequence and analysis of human chromosome 13.

  PMID 15057823 · PMC2665288 · Nature · 2004 · 8 claims · 8 setups

  Full-text index only

  95.5 Mb of finished sequence from chromosome 13 was completed, containing 633 genes and 296 pseudogenes.

  chromosome rpci-11 genomic comparative fluorescence

• Polymorphix: a sequence polymorphism database.

  PMID 15608242 · PMC540030 · Nucleic acids research · 2005 · 8 claims · 5 setups

  Full-text index only

  Polymorphix is an ACNUC-structured database that organizes EMBL/GenBank sequences into within-species homologous sequence families using similarity and bibliographic criteria, with alignments, outgroups and phylogenetic trees provided.

  eukaryotic clustered consensus aligned sequence blast phylogenetic

• TreeFam: a curated database of phylogenetic trees of animal gene families.

  PMID 16381935 · PMC1347480 · Nucleic acids research · 2006 · 7 claims · 6 setups

  Full-text index only

  Tree-based inference of orthologs and paralogs is more robust than BLAST-based methods because evolutionary rates (and thus pairwise BLAST scores) vary across gene family members

  sequences animal treefam-b lamin phylogenetic homology sequence

• What the Phage: a scalable workflow for the identification and analysis of phage sequences.

  PMID 36399058 · PMC9673492 · GigaScience · 2022 · 8 claims · 7 setups

  Has reproduction · 76

  WtP combines 11 tools (14 approaches) for phage prediction in a parallel, containerized Nextflow workflow

  assembled illumina phage-predicted predicted multitool metagenome gene

• Genetic variation in an individual human exome.

  PMID 18704161 · PMC2493042 · PLoS genetics · 2008 · 8 claims · 7 setups

  Full-text index only

  The ~12,500 nonsilent coding variants in the HuRef exome can be reduced ~8-fold to a set of ~1,600 variants most likely to affect protein function.

  huref genes subset whole-genome allele functional

• Genetic analysis of Leishmania donovani tropism using a naturally attenuated cutaneous strain.

  PMID 24992200 · PMC4081786 · PLoS pathogens · 2014 · 8 claims · 8 setups

  Has reproduction · 63

  The CL-SL L. donovani isolate is severely attenuated for survival in visceral organs (liver, spleen) of BALB/c mice compared with the VL-SL isolate, while inducing transient footpad swelling that VL-SL does not.

  balb cl-sl donovani experimental transgenic genome