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).

• Genome wide identification of recessive cancer genes by combinatorial mutation analysis.

  PMID 18846217 · PMC2557123 · PloS one · 2008 · 7 claims · 4 setups

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  A combinatorial mutation analysis identified 154 candidate recessive cancer genes (pRecessiveCancer<1.5x10-7, FDR=0.39)

  refseq tp53 tumor 154-gene est paired array

• Recent segmental and gene duplications in the mouse genome.

  PMID 12914656 · PMC193640 · Genome biology · 2003 · 8 claims · 8 setups

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  33.6 Mb (1.2%) of the February 2003 mouse genome assembly (2,695 Mb) is involved in recent segmental duplications

  genome gene ensembl-annotated chromosome pairwise gene blat

• Analysis of the prostate cancer cell line LNCaP transcriptome using a sequencing-by-synthesis approach.

  PMID 17010196 · PMC1592491 · BMC genomics · 2006 · 8 claims · 7 setups

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  High-throughput 454 sequencing-by-synthesis of LNCaP cDNA can profile transcript abundance across the transcriptome

  lncap lncap-derived r1881-treated massively blast blat

• Discovery of novel human transcript variants by analysis of intronic single-block EST with polyadenylation site.

  PMID 19906316 · PMC2784480 · BMC genomics · 2009 · 8 claims · 7 setups

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  Intronic single-block ESTs with poly(A/T) tails reveal previously unidentified novel transcript variants missed by existing databases.

  genome poly est cdna est blast cdna

• Investigating hookworm genomes by comparative analysis of two Ancylostoma species.

  PMID 15854223 · PMC1112591 · BMC genomics · 2005 · 8 claims · 8 setups

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  Nearly 20,000 ESTs from 7 cDNA libraries define nearly 7,000 hookworm genes across A. caninum and A. ceylanicum

  caninum ceylanicum est bioinformatic functional

• The global landscape of sequence diversity.

  PMID 17996061 · PMC2258180 · Genome biology · 2007 · 7 claims · 5 setups

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  Eukaryotic sequence datasets show substantially greater genetic diversity (higher sequence/gene family discovery rates) than bacterial datasets, likely related to differences in modes of genetic inheritance.

  fully eukaryotic complete gene blast-based est gene

• A novel de novo PAX6 mutation in an Ashkenazi-Jewish family with aniridia.

  PMID 18334930 · PMC2255027 · Molecular vision · 2008 · 7 claims · 5 setups

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  A novel heterozygous de novo PAX6 frameshift mutation (c.577_578insG, insG@Gly72) in exon 6 causes autosomal dominant aniridia with congenital cataract, nystagmus, and glaucoma in this family.

  genomic pax6 direct microsatellite blast

• The other side of comparative genomics: genes with no orthologs between the cow and other mammalian species.

  PMID 20003425 · PMC2808326 · BMC genomics · 2009 · 7 claims · 4 setups

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  3,801 bovine genes have no orthologs in human, mouse and dog, and 1,010 human genes have no orthologs in cow despite having orthologs in mouse and dog

  bovine cow coding blast-based ensembl gene

• Database resources of the National Center for Biotechnology Information.

  PMID 17170002 · PMC1781113 · Nucleic acids research · 2007 · 8 claims · 8 setups

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  NCBI maintains an integrated suite of database resources (Entrez, PubMed, RefSeq, dbSNP, BLAST, etc.) for molecular biology data retrieval and analysis

  genbank genomic eukaryotic completely sequence rapid est

• Annotation and analysis of 10,000 expressed sequence tags from developing mouse eye and adult retina.

  PMID 14519200 · PMC328454 · Genome biology · 2003 · 8 claims · 5 setups

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  Annotation of 8,633 high-quality non-mitochondrial/non-ribosomal ESTs shows 57% represent known genes and 43% are unknown or novel, with M15E having the highest proportion of novel ESTs

  embryonic high-quality unique m15e est sequence comparative

• Identification and characterization of insect-specific proteins by genome data analysis.

  PMID 17407609 · PMC1852559 · BMC genomics · 2007 · 8 claims · 7 setups

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  Comparative genome analysis across five holometabolous insects and three non-insect eukaryotes (opisthokonts) identifies 154 insect-specific orthologous groups (refined to 51 proteins) and 466 eukaryote/opisthokont-core orthologous groups

  drosophila insect-core locusta insect-specific comparative est functional

• Non-EST based prediction of exon skipping and intron retention events using Pfam information.

  PMID 16204458 · PMC1243800 · Nucleic acids research · 2005 · 7 claims · 5 setups

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  A novel ab initio method predicts exon skipping and intron retention events using only Pfam domain annotation, via a Viterbi-like dynamic programming algorithm applied to the Pfam alignment.

  refseq dbest genome pfam initio est comparative

• A target enrichment method for gathering phylogenetic information from hundreds of loci: An example from the Compositae.

  PMID 25202605 · PMC4103609 · Applications in plant sciences · 2014 · 8 claims · 8 setups

  Has reproduction · 87

  A custom sequence capture probe set (9678 baits targeting 1061 orthologous genes) was designed to enrich COS loci across the Compositae.

  compositae same species helianthus targeted genome genomic

• Identification and characterization of a novel mammalian Mg2+ transporter with channel-like properties.

  PMID 15804357 · PMC1129089 · BMC genomics · 2005 · 8 claims · 6 setups

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  MagT1 is a novel mammalian Mg2+ transporter with channel-like properties, showing no amino acid sequence identity to other known transporters

  kidney mdct tissues xenopus oligonucleotide northern real-time

• Assessing the gene space in draft genomes.

  PMID 19042974 · PMC2615622 · Nucleic acids research · 2009 · 6 claims · 7 setups

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  The proportion of mapped CEGs in a draft genome assembly is a useful metric for describing gene space completeness, complementing N50 and x-fold coverage.

  caenorhabditis toxoplasma homo briggsae cegma blast tblastn