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.

  • Navarro-Muñoz JC*, Selem-Mojica N*, Mullowney M*, Kautsar S, Tryon H, Parkinson E, De Los Santos ELC, Yeong M, Cruz-Morales P, Abubucker S, Roeters A, Lokhorst W, Fernandez-Guerra A, Dias Cappelini LT, Thomson R, Metcalf WW, Kelleher NL, Barona Gomez F, Medema MH (2018) A computational framework for systematic exploration of biosynthetic diversity from large-scale genomic data. BioRxiv, doi: 10.1101/445270 [PDF]
  • Carrion VJ, Cordovez V, Tyc O, Etalo DW, de Bruijn I, de Jager VCL, Medema MH, Eberl L, Raaijmakers JM (2018) Involvement of Burkholderiaceae and sulfurous volatiles in disease-suppressive soils. ISME J 12(9): 2307-2321. [PDF]
  • Bahram M, Hildebrand F, Forslund SK, Anderson JL, Soudzilovskaia NA, Bodegom PM, Bengtsson-Palme J, Anslan S, Coelho LP, Harend H, Huerta-Cepas J, Medema MH, Maltz MR, Mundra S, Olsson PA, Pent M, Polme S, Sunagawa S, Ryberg M, Tedersoo L, Bork P (2018) Structure and function of the global topsoil microbiome. Nature 560(7717): 233-237. [PDF]
  • Epstein SC, Charkoudian LK, Medema MH (2018) A standardized workflow for submitting data to the Minimum Information about a Biosynthetic Gene cluster (MIBiG) repository: prospects for research-based educational experiences. Stand Genomic Sci 13: 16. [PDF]
  • Hoogendoorn K, Barra L, Waalwijk C, Dickschat JS, van der Lee TAJ, Medema MH (2018) Evolution and Diversity of Biosynthetic Gene Clusters in Fusarium. Front Microbiol 9: 1158. [PDF]
  • Oyserman BO, Medema MH, Raaijmakers JM (2018) Road MAPs to engineer host microbiomes. Curr Opin Microbiol 43: 46-54. [PDF]
  • Sosio M, Gaspari E, Iorio M, Pessina S, Medema MH, Bernasconi A, Simone M, Maffioli SI, Ebright RH, Donadio S (2018) Analysis of the Pseudouridimycin Biosynthetic Pathway Provides Insights into the Formation of C-nucleoside Antibiotics. Cell Chem Biol 25(5): 540-549.e4. [PDF]
  • Harvey CJB, Tang M, Schlecht U, Horecka J, Fischer CR, Lin HC, Li J, Naughton B, Cherry J, Miranda M, Li YF, Chu AM, Hennessy JR, Vandova GA, Inglis D, Aiyar RS, Steinmetz LM, Davis RW, Medema MH, Sattely E, Khosla C, St Onge RP, Tang Y, Hillenmeyer ME (2018) HEx: A heterologous expression platform for the discovery of fungal natural products. Sci Adv 4(4): eaar5459. [PDF]
  • Loureiro C, Medema MH, van der Oost J, Sipkema D (2018) Exploration and exploitation of the environment for novel specialized metabolites. Curr Opin Biotechnol 50: 206-213. [PDF]
  • Casini A, Chang FY, Eluere R, King AM, Young EM, Dudley QM, Karim A, Pratt K, Bristol C, Forget A, Ghodasara A, Warden-Rothman R, Gan R, Cristofaro A, Borujeni AE, Ryu MH, Li J, Kwon YC, Wang H, Tatsis E, Rodriguez-Lopez C, O'Connor S, Medema MH, Fischbach MA, Jewett MC, Voigt C, Gordon DB (2018) A Pressure Test to Make 10 Molecules in 90 Days: External Evaluation of Methods to Engineer Biology. J Am Chem Soc 140(12): 4302-4316. [PDF]
  • Brotherton CA, Medema MH, Greenberg EP (2018) luxR Homolog-Linked Biosynthetic Gene Clusters in Proteobacteria. mSystems 3(3). [PDF]
  • Medema MH (2018) Computational Genomics of Specialized Metabolism: from Natural Product Discovery to Microbiome Ecology. mSystems 3(2): . [PDF]
  • Haas KL, Heemstra JM, Medema MH, Charkoudian LK (2018) Collaborating with Undergraduates To Contribute to Biochemistry Community Resources. Biochemistry 57(4): 383-389. [PDF]
  • Kautsar SA, Suarez Duran HG, Medema MH (2018) Genomic Identification and Analysis of Specialized Metabolite Biosynthetic Gene Clusters in Plants Using PlantiSMASH. Methods Mol Biol 1795: 173-188. [PDF]
  • Blin K, Kim HU, Medema MH, Weber T (2017) Recent development of antiSMASH and other computational approaches to mine secondary metabolite biosynthetic gene clusters. Brief Bioinform : . [PDF]
  • Cheng X, Etalo DW, van de Mortel JE, Dekkers E, Nguyen L, Medema MH, Raaijmakers JM (2017) Genome-wide analysis of bacterial determinants of plant growth promotion and induced systemic resistance by Pseudomonas fluorescens. Environ Microbiol 19(11): 4638-4656. [PDF]
  • Chevrette MG, Aicheler F, Kohlbacher O, Currie CR, Medema MH (2017) SANDPUMA: ensemble predictions of nonribosomal peptide chemistry reveal biosynthetic diversity across Actinobacteria. Bioinformatics 33(20): 3202-3210. [PDF]
  • Ceniceros A, Dijkhuizen L, Petrusma M, Medema MH (2017) Genome-based exploration of the specialized metabolic capacities of the genus Rhodococcus. BMC Genomics 18(1): 593. [PDF]
  • Huang AC, Kautsar SA, Hong YJ, Medema MH, Bond AD, Tantillo DJ, Osbourn A (2017) Unearthing a sesterterpene biosynthetic repertoire in the Brassicaceae through genome mining reveals convergent evolution. Proc Natl Acad Sci U S A 114(29): E6005-E6014. [PDF]
  • Blin K, Wolf T, Chevrette MG, Lu X, Schwalen CJ, Kautsar SA, Suarez Duran HG, de Los Santos ELC, Kim HU, Nave M, Dickschat JS, Mitchell DA, Shelest E, Breitling R, Takano E, Lee SY, Weber T, Medema MH (2017) antiSMASH 4.0-improvements in chemistry prediction and gene cluster boundary identification. Nucleic Acids Res 45(W1): W36-W41. [PDF]
  • Kautsar SA*, Suarez Duran HG*, Blin K, Osbourn A, Medema MH (2017) plantiSMASH: automated identification, annotation and expression analysis of plant biosynthetic gene clusters. Nucleic Acids Res 45(W1): W55-W63. [PDF]
  • Gaiser RA, Medema MH, Kleerebezem M, van Baarlen P, Wells JM (2017) Draft Genome Sequence of a Porcine Commensal, Rothia nasimurium, Encoding a Nonribosomal Peptide Synthetase Predicted To Produce the Ionophore Antibiotic Valinomycin. Genome Announc 5(22): . [PDF]
  • Tracanna V, de Jong A, Medema MH, Kuipers OP (2017) Mining prokaryotes for antimicrobial compounds: from diversity to function. FEMS Microbiol Rev 41(3): 417-429. [PDF]
  • Blin K, Medema MH, Kottmann R, Lee SY, Weber T (2017) The antiSMASH database, a comprehensive database of microbial secondary metabolite biosynthetic gene clusters. Nucleic Acids Res 45(D1): D555-D559. [PDF]
  • Nguyen DD, Melnik AV, Koyama N, Lu X, Schorn M, Fang J, Aguinaldo K, Lincecum TL Jr, Ghequire MG, Carrion VJ, Cheng TL, Duggan BM, Malone JG, Mauchline TH, Sanchez LM, Kilpatrick AM, Raaijmakers JM, De Mot R, Moore BS, Medema MH, Dorrestein PC (2016) Indexing the Pseudomonas specialized metabolome enabled the discovery of poaeamide B and the bananamides. Nat Microbiol 2: 16197. [PDF]
  • Medema MH, Zhao H (2016) Editorial: Synthetic biology and bioinformatics. Nat Prod Rep 33(8): 913-4. [PDF]
  • Medema MH, Osbourn A (2016) Computational genomic identification and functional reconstitution of plant natural product biosynthetic pathways. Nat Prod Rep 33(8): 951-62. [PDF]
  • Zhao H, Medema MH (2016) Standardization for natural product synthetic biology. Nat Prod Rep 33(8): 920-4. [PDF]
  • Li YF, Tsai KJS, Harvey CJB, Li JJ, Ary BE, Berlew EE, Boehman BL, Findley DM, Friant AG, Gardner CA, Gould MP, Ha JH, Lilley BK, McKinstry EL, Nawal S, Parry RC, Rothchild KW, Silbert SD, Tentilucci MD, Thurston AM, Wai RB, Yoon Y, Aiyar RS, Medema MH, Hillenmeyer ME, Charkoudian LK (2016) Comprehensive curation and analysis of fungal biosynthetic gene clusters of published natural products. Fungal Genet Biol 89: 18-28. [PDF]
  • van der Lee TAJ, Medema MH (2016) Computational strategies for genome-based natural product discovery and engineering in fungi. Fungal Genet Biol 89: 29-36. [PDF]
  • Wu C, Medema MH, Lakamp RM, Zhang L, Dorrestein PC, Choi YH, van Wezel GP (2016) Leucanicidin and Endophenasides Result from Methyl-Rhamnosylation by the Same Tailoring Enzymes in Kitasatospora sp. MBT66. ACS Chem Biol 11(2): 478-90. [PDF]
  • Salo OV, Ries M, Medema MH, Lankhorst PP, Vreeken RJ, Bovenberg RA, Driessen AJ (2015) Genomic mutational analysis of the impact of the classical strain improvement program on beta-lactam producing Penicillium chrysogenum. BMC Genomics 16: 937. [PDF]
  • 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]
  • Diez V, Loznik M, Taylor S, Winn M, Rattray NJ, Podmore H, Micklefield J, Goodacre R, Medema MH, Muller U, Bovenberg R, Janssen DB, Takano E (2015) Functional Exchangeability of Oxidase and Dehydrogenase Reactions in the Biosynthesis of Hydroxyphenylglycine, a Nonribosomal Peptide Building Block. ACS Synth Biol 4(7): 796-807. [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