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Items: 1 to 50 of 59

1.

Structure and function of the global topsoil microbiome.

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, Põlme S, Sunagawa S, Ryberg M, Tedersoo L, Bork P.

Nature. 2018 Aug;560(7717):233-237. doi: 10.1038/s41586-018-0386-6. Epub 2018 Aug 1.

PMID:
30069051
2.

A standardized workflow for submitting data to the Minimum Information about a Biosynthetic Gene cluster (MIBiG) repository: prospects for research-based educational experiences.

Epstein SC, Charkoudian LK, Medema MH.

Stand Genomic Sci. 2018 Jul 11;13:16. doi: 10.1186/s40793-018-0318-y. eCollection 2018.

3.

Evolution and Diversity of Biosynthetic Gene Clusters in Fusarium.

Hoogendoorn K, Barra L, Waalwijk C, Dickschat JS, van der Lee TAJ, Medema MH.

Front Microbiol. 2018 Jun 5;9:1158. doi: 10.3389/fmicb.2018.01158. eCollection 2018.

4.

Involvement of Burkholderiaceae and sulfurous volatiles in disease-suppressive soils.

Carrión VJ, Cordovez V, Tyc O, Etalo DW, de Bruijn I, de Jager VCL, Medema MH, Eberl L, Raaijmakers JM.

ISME J. 2018 Jun 13. doi: 10.1038/s41396-018-0186-x. [Epub ahead of print]

PMID:
29899517
5.

Genomic Identification and Analysis of Specialized Metabolite Biosynthetic Gene Clusters in Plants Using PlantiSMASH.

Kautsar SA, Suarez Duran HG, Medema MH.

Methods Mol Biol. 2018;1795:173-188. doi: 10.1007/978-1-4939-7874-8_15.

PMID:
29846928
6.

HEx: A heterologous expression platform for the discovery of fungal natural products.

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.

Sci Adv. 2018 Apr 11;4(4):eaar5459. doi: 10.1126/sciadv.aar5459. eCollection 2018 Apr.

7.

luxR Homolog-Linked Biosynthetic Gene Clusters in Proteobacteria.

Brotherton CA, Medema MH, Greenberg EP.

mSystems. 2018 Mar 27;3(3). pii: e00208-17. doi: 10.1128/mSystems.00208-17. eCollection 2018 May-Jun.

8.

Computational Genomics of Specialized Metabolism: from Natural Product Discovery to Microbiome Ecology.

Medema MH.

mSystems. 2018 Mar 6;3(2). pii: e00182-17. doi: 10.1128/mSystems.00182-17. eCollection 2018 Mar-Apr.

9.

Analysis of the Pseudouridimycin Biosynthetic Pathway Provides Insights into the Formation of C-nucleoside Antibiotics.

Sosio M, Gaspari E, Iorio M, Pessina S, Medema MH, Bernasconi A, Simone M, Maffioli SI, Ebright RH, Donadio S.

Cell Chem Biol. 2018 May 17;25(5):540-549.e4. doi: 10.1016/j.chembiol.2018.02.008. Epub 2018 Mar 15.

PMID:
29551347
10.

A Pressure Test to Make 10 Molecules in 90 Days: External Evaluation of Methods to Engineer Biology.

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.

J Am Chem Soc. 2018 Mar 28;140(12):4302-4316. doi: 10.1021/jacs.7b13292. Epub 2018 Mar 16.

PMID:
29480720
11.

Exploration and exploitation of the environment for novel specialized metabolites.

Loureiro C, Medema MH, van der Oost J, Sipkema D.

Curr Opin Biotechnol. 2018 Apr;50:206-213. doi: 10.1016/j.copbio.2018.01.017. Epub 2018 Feb 14. Review.

PMID:
29454184
12.

Road MAPs to engineer host microbiomes.

Oyserman BO, Medema MH, Raaijmakers JM.

Curr Opin Microbiol. 2018 Jun;43:46-54. doi: 10.1016/j.mib.2017.11.023. Epub 2017 Dec 5. Review.

13.

Recent development of antiSMASH and other computational approaches to mine secondary metabolite biosynthetic gene clusters.

Blin K, Kim HU, Medema MH, Weber T.

Brief Bioinform. 2017 Nov 3. doi: 10.1093/bib/bbx146. [Epub ahead of print]

PMID:
29112695
14.

Collaborating with Undergraduates To Contribute to Biochemistry Community Resources.

Haas KL, Heemstra JM, Medema MH, Charkoudian LK.

Biochemistry. 2018 Jan 30;57(4):383-389. doi: 10.1021/acs.biochem.7b00872. Epub 2017 Nov 2.

PMID:
29048882
15.

Genome-wide analysis of bacterial determinants of plant growth promotion and induced systemic resistance by Pseudomonas fluorescens.

Cheng X, Etalo DW, van de Mortel JE, Dekkers E, Nguyen L, Medema MH, Raaijmakers JM.

Environ Microbiol. 2017 Nov;19(11):4638-4656. doi: 10.1111/1462-2920.13927. Epub 2017 Nov 2.

PMID:
28892231
16.

Genome-based exploration of the specialized metabolic capacities of the genus Rhodococcus.

Ceniceros A, Dijkhuizen L, Petrusma M, Medema MH.

BMC Genomics. 2017 Aug 9;18(1):593. doi: 10.1186/s12864-017-3966-1.

17.

Unearthing a sesterterpene biosynthetic repertoire in the Brassicaceae through genome mining reveals convergent evolution.

Huang AC, Kautsar SA, Hong YJ, Medema MH, Bond AD, Tantillo DJ, Osbourn A.

Proc Natl Acad Sci U S A. 2017 Jul 18;114(29):E6005-E6014. doi: 10.1073/pnas.1705567114. Epub 2017 Jul 3.

18.

SANDPUMA: ensemble predictions of nonribosomal peptide chemistry reveal biosynthetic diversity across Actinobacteria.

Chevrette MG, Aicheler F, Kohlbacher O, Currie CR, Medema MH.

Bioinformatics. 2017 Oct 15;33(20):3202-3210. doi: 10.1093/bioinformatics/btx400.

PMID:
28633438
19.

Draft Genome Sequence of a Porcine Commensal, Rothia nasimurium, Encoding a Nonribosomal Peptide Synthetase Predicted To Produce the Ionophore Antibiotic Valinomycin.

Gaiser RA, Medema MH, Kleerebezem M, van Baarlen P, Wells JM.

Genome Announc. 2017 Jun 1;5(22). pii: e00453-17. doi: 10.1128/genomeA.00453-17.

20.

antiSMASH 4.0-improvements in chemistry prediction and gene cluster boundary identification.

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.

Nucleic Acids Res. 2017 Jul 3;45(W1):W36-W41. doi: 10.1093/nar/gkx319.

21.

plantiSMASH: automated identification, annotation and expression analysis of plant biosynthetic gene clusters.

Kautsar SA, Suarez Duran HG, Blin K, Osbourn A, Medema MH.

Nucleic Acids Res. 2017 Jul 3;45(W1):W55-W63. doi: 10.1093/nar/gkx305.

22.

Mining prokaryotes for antimicrobial compounds: from diversity to function.

Tracanna V, de Jong A, Medema MH, Kuipers OP.

FEMS Microbiol Rev. 2017 May 1;41(3):417-429. doi: 10.1093/femsre/fux014. Review.

PMID:
28402441
23.

Erratum: Indexing the Pseudomonas specialized metabolome enabled the discovery of poaeamide B and the bananamides.

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.

Nat Microbiol. 2017 Jan 23;2:17010. doi: 10.1038/nmicrobiol.2017.10. No abstract available.

PMID:
28112718
24.

The antiSMASH database, a comprehensive database of microbial secondary metabolite biosynthetic gene clusters.

Blin K, Medema MH, Kottmann R, Lee SY, Weber T.

Nucleic Acids Res. 2017 Jan 4;45(D1):D555-D559. doi: 10.1093/nar/gkw960. Epub 2016 Oct 24.

25.

Indexing the Pseudomonas specialized metabolome enabled the discovery of poaeamide B and the bananamides.

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.

Nat Microbiol. 2016 Oct 31;2:16197. doi: 10.1038/nmicrobiol.2016.197. Erratum in: Nat Microbiol. 2017 Jan 23;2:17010.

26.

Editorial: Synthetic biology and bioinformatics.

Medema MH, Zhao H.

Nat Prod Rep. 2016 Aug 27;33(8):913-4. doi: 10.1039/c6np90031c. Epub 2016 Jul 20. No abstract available.

PMID:
27438694
27.

Computational genomic identification and functional reconstitution of plant natural product biosynthetic pathways.

Medema MH, Osbourn A.

Nat Prod Rep. 2016 Aug 27;33(8):951-62. doi: 10.1039/c6np00035e. Epub 2016 Jun 20. Review.

28.

Standardization for natural product synthetic biology.

Zhao H, Medema MH.

Nat Prod Rep. 2016 Aug 27;33(8):920-4. doi: 10.1039/c6np00030d. Epub 2016 Jun 17. Review.

29.

Comprehensive curation and analysis of fungal biosynthetic gene clusters of published natural products.

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.

Fungal Genet Biol. 2016 Apr;89:18-28. doi: 10.1016/j.fgb.2016.01.012. Epub 2016 Jan 22.

30.

Computational strategies for genome-based natural product discovery and engineering in fungi.

van der Lee TAJ, Medema MH.

Fungal Genet Biol. 2016 Apr;89:29-36. doi: 10.1016/j.fgb.2016.01.006. Epub 2016 Jan 13. Review.

31.

Leucanicidin and Endophenasides Result from Methyl-Rhamnosylation by the Same Tailoring Enzymes in Kitasatospora sp. MBT66.

Wu C, Medema MH, Läkamp RM, Zhang L, Dorrestein PC, Choi YH, van Wezel GP.

ACS Chem Biol. 2016 Feb 19;11(2):478-90. doi: 10.1021/acschembio.5b00801. Epub 2015 Dec 24.

PMID:
26675041
32.

Genomic mutational analysis of the impact of the classical strain improvement program on β-lactam producing Penicillium chrysogenum.

Salo OV, Ries M, Medema MH, Lankhorst PP, Vreeken RJ, Bovenberg RA, Driessen AJ.

BMC Genomics. 2015 Nov 14;16:937. doi: 10.1186/s12864-015-2154-4.

33.

Computational approaches to natural product discovery.

Medema MH, Fischbach MA.

Nat Chem Biol. 2015 Sep;11(9):639-48. doi: 10.1038/nchembio.1884.

34.

Minimum Information about a Biosynthetic Gene cluster.

Medema MH, Kottmann R, Yilmaz P, Cummings M, Biggins JB, Blin K, de Bruijn I, Chooi YH, Claesen J, Coates RC, Cruz-Morales P, Duddela S, Düsterhus S, Edwards DJ, Fewer DP, Garg N, Geiger C, Gomez-Escribano JP, Greule A, Hadjithomas M, Haines AS, Helfrich EJ, Hillwig ML, Ishida K, Jones AC, Jones CS, Jungmann K, Kegler C, Kim HU, Kötter P, Krug D, Masschelein J, Melnik AV, Mantovani SM, Monroe EA, Moore M, Moss N, Nützmann HW, Pan G, Pati A, Petras D, Reen FJ, Rosconi F, Rui Z, Tian Z, Tobias NJ, Tsunematsu Y, Wiemann P, Wyckoff E, Yan X, Yim G, Yu F, Xie Y, Aigle B, Apel AK, Balibar CJ, Balskus EP, Barona-Gómez F, Bechthold A, Bode HB, Borriss R, Brady SF, Brakhage AA, Caffrey P, Cheng YQ, Clardy J, Cox RJ, De Mot R, Donadio S, Donia MS, van der Donk WA, Dorrestein PC, Doyle S, Driessen AJ, Ehling-Schulz M, Entian KD, Fischbach MA, Gerwick L, Gerwick WH, Gross H, Gust B, Hertweck C, Höfte M, Jensen SE, Ju J, Katz L, Kaysser L, Klassen JL, Keller NP, Kormanec J, Kuipers OP, Kuzuyama T, Kyrpides NC, Kwon HJ, Lautru S, Lavigne R, Lee CY, Linquan B, Liu X, Liu W, Luzhetskyy A, Mahmud T, Mast Y, Méndez C, Metsä-Ketelä M, Micklefield J, Mitchell DA, Moore BS, Moreira LM, Müller R, Neilan BA, Nett M, Nielsen J, O'Gara F, Oikawa H, Osbourn A, Osburne MS, Ostash B, Payne SM, Pernodet JL, Petricek M, Piel J, Ploux O, Raaijmakers JM, Salas JA, Schmitt EK, Scott B, Seipke RF, Shen B, Sherman DH, Sivonen K, Smanski MJ, Sosio M, Stegmann E, Süssmuth RD, Tahlan K, Thomas CM, Tang Y, Truman AW, Viaud M, Walton JD, Walsh CT, Weber T, van Wezel GP, Wilkinson B, Willey JM, Wohlleben W, Wright GD, Ziemert N, Zhang C, Zotchev SB, Breitling R, Takano E, Glöckner FO.

Nat Chem Biol. 2015 Sep;11(9):625-31. doi: 10.1038/nchembio.1890. No abstract available.

35.

antiSMASH 3.0-a comprehensive resource for the genome mining of biosynthetic gene clusters.

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.

Nucleic Acids Res. 2015 Jul 1;43(W1):W237-43. doi: 10.1093/nar/gkv437. Epub 2015 May 6.

36.

Functional Exchangeability of Oxidase and Dehydrogenase Reactions in the Biosynthesis of Hydroxyphenylglycine, a Nonribosomal Peptide Building Block.

Diez V, Loznik M, Taylor S, Winn M, Rattray NJ, Podmore H, Micklefield J, Goodacre R, Medema MH, Müller U, Bovenberg R, Janssen DB, Takano E.

ACS Synth Biol. 2015 Jul 17;4(7):796-807. doi: 10.1021/sb500368w. Epub 2015 Mar 9.

PMID:
25713978
37.

A systematic computational analysis of biosynthetic gene cluster evolution: lessons for engineering biosynthesis.

Medema MH, Cimermancic P, Sali A, Takano E, Fischbach MA.

PLoS Comput Biol. 2014 Dec 4;10(12):e1004016. doi: 10.1371/journal.pcbi.1004016. eCollection 2014 Dec. Erratum in: PLoS Comput Biol. 2016 Mar;12(3):e1004767.

38.

Pep2Path: automated mass spectrometry-guided genome mining of peptidic natural products.

Medema MH, Paalvast Y, Nguyen DD, Melnik A, Dorrestein PC, Takano E, Breitling R.

PLoS Comput Biol. 2014 Sep 4;10(9):e1003822. doi: 10.1371/journal.pcbi.1003822. eCollection 2014 Sep.

39.

Insights into secondary metabolism from a global analysis of prokaryotic biosynthetic gene clusters.

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.

Cell. 2014 Jul 17;158(2):412-421. doi: 10.1016/j.cell.2014.06.034.

40.

MS/MS networking guided analysis of molecule and gene cluster families.

Nguyen DD, Wu 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.

Proc Natl Acad Sci U S A. 2013 Jul 9;110(28):E2611-20. doi: 10.1073/pnas.1303471110. Epub 2013 Jun 24.

41.

antiSMASH 2.0--a versatile platform for genome mining of secondary metabolite producers.

Blin K, Medema MH, Kazempour D, Fischbach MA, Breitling R, Takano E, Weber T.

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W204-12. doi: 10.1093/nar/gkt449. Epub 2013 Jun 3.

42.

Design-based re-engineering of biosynthetic gene clusters: plug-and-play in practice.

Frasch HJ, Medema MH, Takano E, Breitling R.

Curr Opin Biotechnol. 2013 Dec;24(6):1144-50. doi: 10.1016/j.copbio.2013.03.006. Epub 2013 Mar 27. Review.

PMID:
23540422
43.

Detecting sequence homology at the gene cluster level with MultiGeneBlast.

Medema MH, Takano E, Breitling R.

Mol Biol Evol. 2013 May;30(5):1218-23. doi: 10.1093/molbev/mst025. Epub 2013 Feb 14.

44.

MultiMetEval: comparative and multi-objective analysis of genome-scale metabolic models.

Zakrzewski P, Medema MH, Gevorgyan A, Kierzek AM, Breitling R, Takano E.

PLoS One. 2012;7(12):e51511. doi: 10.1371/journal.pone.0051511. Epub 2012 Dec 14.

45.

Complete genome sequence of the frog pathogen Mycobacterium ulcerans ecovar Liflandii.

Tobias NJ, Doig KD, Medema MH, Chen H, Haring V, Moore R, Seemann T, Stinear TP.

J Bacteriol. 2013 Feb;195(3):556-64. doi: 10.1128/JB.02132-12. Epub 2012 Nov 30.

46.

Bioinformatics approaches and software for detection of secondary metabolic gene clusters.

Fedorova ND, Moktali V, Medema MH.

Methods Mol Biol. 2012;944:23-45. doi: 10.1007/978-1-62703-122-6_2.

PMID:
23065606
47.

Metabolomics methods for the synthetic biology of secondary metabolism.

Nguyen QT, Merlo ME, Medema MH, Jankevics A, Breitling R, Takano E.

FEBS Lett. 2012 Jul 16;586(15):2177-83. doi: 10.1016/j.febslet.2012.02.008. Epub 2012 Feb 15. Review.

48.

Computational tools for the synthetic design of biochemical pathways.

Medema MH, van Raaphorst R, Takano E, Breitling R.

Nat Rev Microbiol. 2012 Jan 23;10(3):191-202. doi: 10.1038/nrmicro2717. Review.

PMID:
22266781
49.

The future of industrial antibiotic production: from random mutagenesis to synthetic biology.

Medema MH, Alam MT, Breitling R, Takano E.

Bioeng Bugs. 2011 Jul-Aug;2(4):230-3. doi: 10.1111/j.1751-7915.2010.00226.x. Epub 2011 Jul 1.

PMID:
21829093
50.

Comparative genome-scale metabolic modeling of actinomycetes: the topology of essential core metabolism.

Alam MT, Medema MH, Takano E, Breitling R.

FEBS Lett. 2011 Jul 21;585(14):2389-94. doi: 10.1016/j.febslet.2011.06.014. Epub 2011 Jun 22.

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