Publications

Here you can find an overview of my scientific publications. Select one of the categories at the right to zoom in to specific article types.

  • Medema MH & Fischbach MA (2015) Computational approaches to natural product discovery. Nature Chemical Biology 11: 639-648. [PDF]
  • Medema MH et al. (2015) Minimum Information about a Biosynthetic Gene cluster. Nature Chemical Biology 11: 625-631. [PDF]
  • Weber T, Blin K, Duddela S, Krug D, Kim HU, Bruccoleri R, Lee SY, Fischbach MA, Müller R, Wohlleben W, Breitling R, Takano E, Medema MH (2015) antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters. Nucleic Acids Research 43: W237-W243. [PDF]
  • Medema MH*, Cimermancic P*, Sali A, Takano E, Fischbach MA (2014) A systematic computational analysis of biosynthetic gene cluster evolution: Lessons for engineering biosynthesis. PLoS Computational Biology 10: e1004016. [PDF]
  • Medema MH, Paalvast T, Nguyen DD, Melnik A, Dorrestein PC, Takano E, Breitling R (2014) Pep2Path: Automated mass spectrometry-guided genome mining of peptidic natural products. PLoS Computational Biology 10: e1003822. [PDF]
  • Cimermancic P*, Medema MH*, Claesen J*, Kurita K, Wieland Brown LC, Mavrommatis K, Pati A, Godfrey PA, Koehrsen M, Clardy J, Birren BW, Takano E, Sali A, Linington RG, Fischbach MA (2014) Insights into secondary metabolism from a global analysis of prokaryotic biosynthetic gene clusters. Cell 158: 412-421. [PDF]
  • Nguyen DD, Wua CH, Moree WJ, Lamsa A, Medema MH, Zhao X, Gavilan RG, Aparicio M, Atencio L, Jackson C, Ballesteros J, Sanchez J, Watrous JD, Phelan VV, van de Wiel C, Kersten RD, Mehnaz S, de Mot R, Shank EA, Charusanti P, Nagarajan H, Duggan BM, Moore BS, Bandeira N, Palsson BØ, Pogliano K, Gutiérrez M, Dorrestein PC (2013) MS/MS networking guided analysis of molecule and gene cluster families. Proceedings of the National Academy of Sciences USA 110: E2611-20. [PDF]
  • Blin K, Medema MH, Kazempour D, Fischbach MA, Breitling R, Takano E, Weber T (2013) antiSMASH 2.0--a versatile platform for genome mining of secondary metabolite producers. Nucleic Acids Research 41: W204-W212. [PDF]
  • Frasch HJ, Medema MH, Takano E, Breitling R (2013) Design-based re-engineering of biosynthetic gene clusters: plug-and-play in practice. Current Opinion in Biotechnology, doi:pii: S0958-1669(13)00063-3. [PDF]
  • Medema MH, Takano E, Breitling R (2013) Detecting sequence homology at the gene cluster level with MultiGeneBlast. Molecular Biology and Evolution 30(5):1218-23. [PDF]
  • Zakrzewski P*, Medema MH*, Gevorgyan A, Kierzek AM, Breitling R, Takano E (2012) MultiMetEval: Comparative and Multi-Objective Analysis of Genome-Scale Metabolic Models. PLoS ONE 7: e51511. [PDF]
  • Tobias NJ, Doig KD, Medema MH, Chen H, Haring V, Moore R, Seemann T, Stinear TP (2012) Complete genome sequence of the frog pathogen Mycobacterium ulcerans ecovar Liflandii. Journal of Bacteriology 195(3):556-64. [PDF]
  • Fedorova ND, Moktali V, Medema MH (2012) Bioinformatics approaches and software for detection of secondary metabolic gene clusters. Methods in Molecular Biology 944: 23-45. [PDF]
  • Nguyen QT, Merlo ME, Medema MH, Jankevics A, Breitling R, Takano E (2012) Metabolomics methods for the synthetic biology of secondary metabolism. FEBS Letters 586: 2177-2183. [PDF]
  • Medema MH, van Raaphorst R, Takano E, Breitling R (2012) Computational tools for the synthetic design of biochemical pathways. Nature Reviews Microbiology 10: 191-202. [PDF]
  • Medema MH*, Alam MT*, Breitling R, Takano E (2011) The future of industrial antibiotic production: from random mutagenesis to synthetic biology. Bioengineered Bugs 2(4): 230-233. [PDF]
  • Alam MT, Medema MH, Takano E, Breitling R (2011) Comparative genome-scale metabolic modeling of actinomycetes: The topology of essential core metabolism. FEBS Letters 585(14): 2389-2394. [PDF]
  • 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 39: W339-W346. [PDF]
  • 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 39: W362-W367. [PDF]
  • Medema MH*, Breitling R, Takano E (2011) Synthetic biology in Streptomyces bacteria. Methods in Enzymology 497: 485-502. [PDF]
  • 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. [PDF]
  • 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. [PDF]
  • 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. [PDF]
  • 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. [PDF]
  • 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. [PDF]
  • 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. [PDF]

*Contributed equally