User:Marnix H. Medema

Contact Info



 * Marnix H. Medema
 * University of Groningen
 * Nijenborgh 7
 * 9747 AG Groningen
 * The Netherlands
 * Email me through OpenWetWare

I work in the Department of Microbial Physiology and the Groningen Bioinformatics Centre at the University of Groningen, as a Ph.D. student on a project on genome mining and synthetic biology of microbial secondary metabolites.

Education

 * 2009 - present: Ph.D. Student, University of Groningen
 * 2008, M.Sc. Biomolecular Sciences, University of Groningen
 * 2006, B.Sc. Biology, Radboud University Nijmegen

Research interests

 * 1) Comparative and Evolutionary Genomics
 * 2) Antibiotics, Natural Products
 * 3) Synthetic Biology
 * 4) Streptomyces Biology

Publications
Medema MH*, Alam MT*, Breitling R, Takano E (2011) The future of industrial antibiotic production: from random mutagenesis to synthetic biology. Bioengineered Bugs, in press  Alam MT, Medema MH, Takano E, Breitling R (2011) Comparative genome-scale metabolic modeling of actinomycetes: The topology of essential core metabolism. FEBS Letters, in press  Medema MH, Blin K, Cimermancic P, de Jager V, Zakrzewski P, Fischbach MA, Weber T, Takano E, Breitling R (2011) antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences. Nucleic Acids Research, advance access  Röttig M, Medema MH, Blin K, Rausch C, Weber T, Kohlbacher O (2011) NRPSPredictor2 -- a web server for predicting NRPS adenylation domain specificity. Nucleic Acids Research, advance access.  Medema MH*, Breitling R, Takano E (2011) Synthetic biology in Streptomyces bacteria. Methods in Enzymology 497: 485-502.  <li>Medema MH*, Alam MT*, Heijne WH, van den Berg MA, Müller U, Trefzer A, Bovenberg RA, Breitling R, Takano E (2011) Genome-wide gene expression changes in an industrial clavulanic acid overproduction strain of Streptomyces clavuligerus. Microbial Biotechnology 4(2): 300-305. </ul> <li>Medema MH, Breitling R, Bovenberg R, Takano E (2011) Exploiting plug-and-play synthetic biology for drug discovery and production in microorganisms. Nature Reviews Microbiology 9(2): 131-137. </ul> <li>Medema MH, Trefzer A, Kovalchuk A, van den Berg M, Müller U, Heijne W, Wu L, Alam MT, Ronning CM, Nierman WC, Bovenberg RA, Breitling R, Takano E (2010) The sequence of a 1.8-mb bacterial linear plasmid reveals a rich evolutionary reservoir of secondary metabolic pathways. Genome Biology and Evolution 2: 212-224. </ul> <li>Medema MH*, Zhou M*, van Hijum SA, Gloerich J, Wessels HJ, Siezen RJ, Strous M (2010) A predicted physicochemically distinct sub-proteome associated with the intracellular organelle of the anammox bacterium Kuenenia stuttgartiensis. BMC Genomics 11: 299. </ul> <li>van Hijum SA*, Medema MH*, Kuipers OP (2009) Mechanisms and evolution of control logic in prokaryotic transcriptional regulation. Microbiology and Molecular Biology Reviews 73(3): 481-509. </ul> <li>Ettwig KF, Shima S, van de Pas-Schoonen KT, Kahnt J, Medema MH, Op den Camp HJ, Jetten MS, Strous M (2008) Denitrifying bacteria anaerobically oxidize methane in the absence of Archaea. Environmental Microbiology 10(11): 3164-3173. </ul>

*Contributed equally