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Sökning: WFRF:(Erlendsson Björn) > Tidskriftsartikel

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1.
  • Olsson, Björn, et al. (författare)
  • Deriving pathway maps from automated text analysis using a grammar-based approach
  • 2006
  • Ingår i: Journal of Bioinformatics and Computational Biology. - : World Scientific. - 0219-7200 .- 1757-6334. ; 4:2, s. 483-501
  • Tidskriftsartikel (refereegranskat)abstract
    • We demonstrate how automated text analysis can be used to support the large-scale analysis of metabolic and regulatory pathways by deriving pathway maps from textual descriptions found in the scientific literature. The main assumption is that correct syntactic analysis combined with domain-specific heuristics provides a good basis for relation extraction. Our method uses an algorithm that searches through the syntactic trees produced by a parser based on a Referent Grammar formalism, identifies relations mentioned in the sentence, and classifies them with respect to their semantic class and epistemic status (facts, counterfactuals, hypotheses). The semantic categories used in the classification are based on the relation set used in KEGG (Kyoto Encyclopedia of Genes and Genomes), so that pathway maps using KEGG notation can be automatically generated. We present the current version of the relation extraction algorithm and an evaluation based on a corpus of abstracts obtained from PubMed. The results indicate that the method is able to combine a reasonable coverage with high accuracy. We found that 61% of all sentences were parsed, and 97% of the parse trees were judged to be correct. The extraction algorithm was tested on a sample of 300 parse trees and was found to produce correct extractions in 90.5% of the cases.
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2.
  • Erlendsson, Lýður S, et al. (författare)
  • Barley as a green factory for the production of functional Flt3 ligand
  • 2009
  • Ingår i: Biotechnology Journal. - Weinheim : Wiley-VCH Verlag GmbH & Co. KGaA. - 1860-7314 .- 1860-6768. ; 5:2, s. 163-171
  • Tidskriftsartikel (refereegranskat)abstract
    • Biologically active recombinant human Flt3 ligand was expressed and isolated from transgenic barley seeds. Its expression is controlled by a tissue specific promoter that confines accumulation of the recombinant protein to the endosperm tissue of the seed. The recombinant Flt3 ligand variant expressed in the seeds contains an HQ-tag for affinity purification on immobilized metal ion affinity chromatography (IMAC) resin. The tagged protein was purified from seed extracts to near homogeneity using sequential chromatography on IMAC affinity resin and cation exchange resin. We also show that the recombinant Flt3 ligand protein undergoes posttranslational modifications: it is a glycoprotein containing alpha-1,3-fucose and alpha-1,2-xylose. The HQ-tagged Flt3 ligand variant exhibits comparable biological activity to commercial Flt3 ligand. This is the first report showing expression and accumulation of recombinant human growth factor in barley seeds with a yield of active protein similar to a bacterial expression system. The present results demonstrate that plant molecular farming is a viable approach for the bioproduction of human-derived growth factors.
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