Data integration in microbial genomics ... - Jacobs University

18 1. Introduction
Doug Wendel, Owen White, Andrew Whiteley, Andreas Wilke, Jennifer
R Wortman, Tanya Yatsunenko and Frank Oliver Glöckner
Submitted to: nature biotechnology, accepted April 2011
Personal Contribution: Initial talk with the title: “Survey results:
MInimal list of contextual data fields for ENvironmental Sequences
(MIENS)” at the 6th meeting of the GSC at the EBI (Hinxton, UK)
October 2008, which was the starting point for the development of this
standard, that was later renamed to MIMARKS. Contributed suggestions
for improvements of the data fields, during implementation work
of this standard in the tools MetaBar and CDinFusion.
Relevance: Standards development for contextual data.
4) Megx.net - Integrated database resource for marine ecological
genomics
Authors: Renzo Kottmann, Ivaylo Kostadinov, Melissa Beth Duhaime,
Pier Luigi Buttigieg, Pelin Yilmaz, Wolfgang Hankeln, Frank Oliver
Glöckner
Published in: Nucleic Acids Research, October 2010
Personal Contribution: Involvement in the web portal design and
programming, bug fixing and improvement of the environmental data
layers in the Genes Mapserver (with Renzo Kottmann, Ivaylo Kostadinov,
Pier Luigi Buttigieg, Pelin Yilmaz).
Relevance: To enhance the core megx.net concept to the research
platform of the Microbial Genomics Group at Max Planck Institute
for Marine Microbiology.
5) Ecological perspectives on domains of unknown function:
a marine point of view
Authors: Pier Luigi Buttigieg, Wolfgang Hankeln, Melissa Beth
Duhaime, Ivaylo Kostadinov, Renzo Kottmann, Pelin Yilmaz, Frank
Oliver Glöckner
Submitted to: ISME Journal, January 2011
Personal Contribution: Helped to analyse the data after HMM
calculations by generating network graphs together with Pier Luigi
Buttigieg.
Relevance: Generating hypothesis about the possible functions of
protein domains in silico, based on their co-occurrence patterns and