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research notebook of Pawel Szczesny

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Libraries to visualize phylogenetic trees

Miniproject to be done: a script to show a biodiversity of metagenomic sample on a taxonomic tree. There are quite a few options to visualize phylogenetic trees in a programmatic way. See summary by Kat Holt. Out of three (four)… Read more ›

Mar 23, 2013
Pawel Szczesny
bioinformatics
libraries, programming, python

Biodiversity analysis on the basis of 16S rRNA

There are many papers describing bias of amplification of 16S gene and resulting bias in assessment of biodiversity. However some interesting recent publications expand the story. There’s a nice research on including number of 16S gene copies per genome into… Read more ›

Mar 21, 2013
Pawel Szczesny
bioinformatics
16S rRNA, biodiversity, NGS
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Recent entries

  • Notes on PMR’s “Is Figshare Open?”
  • Role of ribosomal proteins in Diamond-Blackfan anemia 1
  • Annotations notes – Dephosphorylation of 2,3-bisphosphoglycerate by MIPP expands the regulatory capacity of the Rapoport-Luebering glycolytic shunt.
  • Tweaking solutions in the open
  • Non-model organism – annotations in Bioconductor
  • Consensus sequence from mapping
  • Zotpress, Kcite and PMID Citation Plus
  • Workflow schema for content input, storage and reuse
  • Alternative Splicing and Subfunctionalization Generates Functional Diversity in Fungal Proteomes
  • Elsevier’s profits

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  • April 2015 (3)
  • March 2013 (9)

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