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).

• The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets.

  PMID 19654113 · PMC2759552 · Bioinformatics (Oxford, England) · 2009 · 7 claims · 2 setups

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  IGB is an open-source, Java-based desktop genome browser supporting real-time zooming/panning, moveable tiered feature layout, incremental or genome-scale data loading, and dynamic genome graphs

  arabidopsis pyrosequencing expression

• Phylogenetic profiling of the Arabidopsis thaliana proteome: what proteins distinguish plants from other organisms?

  PMID 15287975 · PMC507878 · Genome biology · 2004 · 8 claims · 6 setups

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  3,848 Arabidopsis proteins were identified as likely plant-specific based on phylogenetic profiling and EST confirmation in multiple plant species

  arabidopsis phylogenetic tblastn subcellular

• Proceedings of the First International Conference on Phylogenomics. March 15-19, 2006. Quebec, Canada.

  PMID 17288567 · PMC1796603 · BMC evolutionary biology · 2007 · 8 claims · 8 setups

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  Gene tree parsimony applied to EST data with widespread gene duplication can infer an organismal phylogeny in excellent agreement with the expected angiosperm phylogeny.

  angiosperms animal oryza proteobacteria gene site-heterogeneous codon

• Analysis of expressed sequence tags from Actinidia: applications of a cross species EST database for gene discovery in the areas of flavor, health, color and ripening.

  PMID 18655731 · PMC2515324 · BMC genomics · 2008 · 7 claims · 6 setups

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  A collection of 132,577 ESTs from four Actinidia species was generated and clustered into 41,858 non-redundant clusters (18,070 TCs and 23,788 singletons)

  cdna full-length tentative non-redundant est codon snp

• Comparative analysis of plant genomes allows the definition of the "Phytolongins": a novel non-SNARE longin domain protein family.

  PMID 19889231 · PMC2779197 · BMC genomics · 2009 · 8 claims · 6 setups

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  A novel, plant-specific family of longin-related proteins, the 'Phytolongins', was identified in land plant genomes.

  genomes longin plant phytolongin iterative phylogenetic genomic

• The TIGR Gene Indices: clustering and assembling EST and known genes and integration with eukaryotic genomes.

  PMID 15608288 · PMC540018 · Nucleic acids research · 2005 · 8 claims · 8 setups

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  The TIGR Gene Indices (TGI) are a collection of 77 species-specific databases that cluster and assemble EST and known gene sequences into tentative consensus (TC) sequences to identify and characterize expressed transcripts.

  est clustered sequences sequence est sequence orf

• Accurate splice site prediction using support vector machines.

  PMID 18269701 · PMC2230508 · BMC bioinformatics · 2007 · 8 claims · 5 setups

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  Weighted degree (WD) kernel SVMs outperform Markov Chains, GeneSplicer and SpliceMachine for genome-wide splice site recognition

  nn269 dgsplicer caenorhabditis arabidopsis svm genome-wide

• Phenotypic variation meets systems biology.

  PMID 19664197 · PMC2745761 · Genome biology · 2009 · 8 claims · 8 setups

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  Cellular differentiation states are constrained by complex networks with substantial positive and negative regulation, challenging the concept of single 'master regulators'

  thp-1 arabidopsis unspecified mammalian deepcage protein-protein sequencing

• DDBJ dealing with mass data produced by the second generation sequencer.

  PMID 18927114 · PMC2686496 · Nucleic acids research · 2009 · 8 claims · 7 setups

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  DDBJ collected and released 2,368,110 entries (1,415,106,598 bases) of original DNA sequence data from July 2007 to June 2008.

  plasmodium oryzias gut drosophila solexa wgs metagenomic