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Items: 1 to 50 of 71

1.

Pathogen-induced activation of disease-suppressive functions in the endophytic root microbiome.

Carrión VJ, Perez-Jaramillo J, Cordovez V, Tracanna V, de Hollander M, Ruiz-Buck D, Mendes LW, van Ijcken WFJ, Gomez-Exposito R, Elsayed SS, Mohanraju P, Arifah A, van der Oost J, Paulson JN, Mendes R, van Wezel GP, Medema MH, Raaijmakers JM.

Science. 2019 Nov 1;366(6465):606-612. doi: 10.1126/science.aaw9285.

PMID:
31672892
2.

MIBiG 2.0: a repository for biosynthetic gene clusters of known function.

Kautsar SA, Blin K, Shaw S, Navarro-Muñoz JC, Terlouw BR, van der Hooft JJJ, van Santen JA, Tracanna V, Suarez Duran HG, Pascal Andreu V, Selem-Mojica N, Alanjary M, Robinson SL, Lund G, Epstein SC, Sisto AC, Charkoudian LK, Collemare J, Linington RG, Weber T, Medema MH.

Nucleic Acids Res. 2019 Oct 15. pii: gkz882. doi: 10.1093/nar/gkz882. [Epub ahead of print]

PMID:
31612915
3.

Assessing Specialized Metabolite Diversity in the Cosmopolitan Plant Genus Euphorbia L.

Ernst M, Nothias LF, van der Hooft JJJ, Silva RR, Saslis-Lagoudakis CH, Grace OM, Martinez-Swatson K, Hassemer G, Funez LA, Simonsen HT, Medema MH, Staerk D, Nilsson N, Lovato P, Dorrestein PC, Rønsted N.

Front Plant Sci. 2019 Jul 2;10:846. doi: 10.3389/fpls.2019.00846. eCollection 2019.

4.

MolNetEnhancer: Enhanced Molecular Networks by Integrating Metabolome Mining and Annotation Tools.

Ernst M, Kang KB, Caraballo-Rodríguez AM, Nothias LF, Wandy J, Chen C, Wang M, Rogers S, Medema MH, Dorrestein PC, van der Hooft JJJ.

Metabolites. 2019 Jul 16;9(7). pii: E144. doi: 10.3390/metabo9070144.

5.

Computer-aided re-engineering of nonribosomal peptide and polyketide biosynthetic assembly lines.

Alanjary M, Cano-Prieto C, Gross H, Medema MH.

Nat Prod Rep. 2019 Sep 1;36(9):1249-1261. doi: 10.1039/c9np00021f. Epub 2019 Jul 1.

PMID:
31259995
6.

BiosyntheticSPAdes: reconstructing biosynthetic gene clusters from assembly graphs.

Meleshko D, Mohimani H, Tracanna V, Hajirasouliha I, Medema MH, Korobeynikov A, Pevzner PA.

Genome Res. 2019 Aug;29(8):1352-1362. doi: 10.1101/gr.243477.118. Epub 2019 Jun 3.

PMID:
31160374
7.

antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline.

Blin K, Shaw S, Steinke K, Villebro R, Ziemert N, Lee SY, Medema MH, Weber T.

Nucleic Acids Res. 2019 Jul 2;47(W1):W81-W87. doi: 10.1093/nar/gkz310.

8.

A genetical metabolomics approach for bioprospecting plant biosynthetic gene clusters.

Witjes L, Kooke R, van der Hooft JJJ, de Vos RCH, Keurentjes JJB, Medema MH, Nijveen H.

BMC Res Notes. 2019 Apr 2;12(1):194. doi: 10.1186/s13104-019-4222-3.

9.

Computational identification of co-evolving multi-gene modules in microbial biosynthetic gene clusters.

Del Carratore F, Zych K, Cummings M, Takano E, Medema MH, Breitling R.

Commun Biol. 2019 Feb 28;2:83. doi: 10.1038/s42003-019-0333-6. eCollection 2019.

10.

Comprehensive mass spectrometry-guided phenotyping of plant specialized metabolites reveals metabolic diversity in the cosmopolitan plant family Rhamnaceae.

Kang KB, Ernst M, van der Hooft JJJ, da Silva RR, Park J, Medema MH, Sung SH, Dorrestein PC.

Plant J. 2019 Jun;98(6):1134-1144. doi: 10.1111/tpj.14292. Epub 2019 Mar 25.

PMID:
30786088
11.

Mining bacterial genomes to reveal secret synergy.

Alanjary M, Medema MH.

J Biol Chem. 2018 Dec 28;293(52):19996-19997. doi: 10.1074/jbc.H118.006669.

12.

The antiSMASH database version 2: a comprehensive resource on secondary metabolite biosynthetic gene clusters.

Blin K, Pascal Andreu V, de Los Santos ELC, Del Carratore F, Lee SY, Medema MH, Weber T.

Nucleic Acids Res. 2019 Jan 8;47(D1):D625-D630. doi: 10.1093/nar/gky1060.

13.

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
14.

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.

15.

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.

16.

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 Sep;12(9):2307-2321. doi: 10.1038/s41396-018-0186-x. Epub 2018 Jun 13.

17.

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
18.

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.

19.

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.

20.

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.

21.

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.

22.

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
23.

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
24.

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.

25.

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. 2019 Jul 19;20(4):1103-1113. doi: 10.1093/bib/bbx146.

26.

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.

27.

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
28.

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.

29.

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.

30.

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.

31.

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.

32.

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.

33.

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.

34.

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
35.

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
36.

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.

37.

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.

38.

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
39.

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.

40.

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.

41.

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.

42.

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.

43.

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
44.

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.

45.

Computational approaches to natural product discovery.

Medema MH, Fischbach MA.

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

46.

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.

47.

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.

48.

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
49.

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.

50.

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.

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