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Research Output 2000 2020

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Journal article
2020
5 Downloads (Pure)

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

Kautsar, S. A., Blin, K., Shaw, S., Navarro-Muñoz, J. C., Terlouw, B. R., van der Hooft, J. J. J., van Santen, J. A., Tracanna, V., Suarez Duran, H. G., Pascal Andreu, V., Selem-Mojica, N., Alanjary, M., Robinson, S. L., Lund, G., Epstein, S. C., Sisto, A. C., Charkoudian, L. K., Collemare, J., Linington, R. G., Weber, T. & 1 others, Medema, M. H., 2020, In : Nucleic acids research. 48, p. D454–D458

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
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2019
100 Downloads (Pure)

antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline

Blin, K., Shaw, S., Steinke, K., Villebro, R., Ziemert, N., Lee, S. Y., Medema, M. H. & Weber, T., 2019, In : Nucleic acids research. 87, W2, p. W81-W87 7 p.

Research output: Contribution to journalJournal articleResearchpeer-review

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Antitumor astins originate from the fungal endophyte Cyanodermella asteris living within the medicinal plant Aster tataricus

Schafhauser, T., Jahn, L., Kirchner, N., Kulik, A., Flor, L., Lang, A., Caradec, T., Fewer, D. P., Sivonen, K., van Berkel, W. J. H., Jacques, P., Weber, T., Gross, H., van Pée, K-H., Wohlleben, W. & Ludwig-Müller, J., 2019, In : Proceedings of the National Academy of Sciences of the United States of America. 52, p. 26909-26917

Research output: Contribution to journalJournal articleResearchpeer-review

100 Downloads (Pure)

Depiction of secondary metabolites and antifungal activity of Bacillus velezensis DTU001.

Devi, S., Kiesewalter, H. T., Kovács, R., Frisvad, J. C., Weber, T., Larsen, T. O., Kovács, Á. T. & Ding, L., 2019, In : Synthetic and Systems Biotechnology. 4, 3, p. 142-149 8 p.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
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Genome Mining Approaches to Bacterial Natural Product Discovery

Ziemert, N., Weber, T. & Medema, M. H., 2019, (Accepted/In press) In : Reference Module in Chemistry, Molecular Sciences and Chemical Engineering. 15 p.

Research output: Contribution to journalJournal articleResearchpeer-review

50 Downloads (Pure)

Highly efficient DSB-free base editing for streptomycetes with CRISPR-BEST

Tong, Y., Whitford, C. M., Robertsen, H. L., Blin, K., Jørgensen, T. S., Klitgaard, A. K., Gren, T., Jiang, X., Weber, T. & Lee, S. Y., 2019, In : Proceedings of the National Academy of Sciences of the United States of America. 116, 41, p. 20366-20375

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
240 Downloads (Pure)

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

Blin, K., Kim, H. U., Medema, M. H. & Weber, T., 2019, In : Briefings in Bioinformatics. 20, 4, p. 1103-1113

Research output: Contribution to journalJournal articleResearchpeer-review

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Sequence-based classification of type II polyketide synthase biosynthetic gene clusters for antiSMASH

Villebro, R., Shaw, S., Blin, K. & Weber, T., 2019, In : Journal of Industrial Microbiology and Biotechnology. 46, 3-4, p. 469-475

Research output: Contribution to journalJournal articleResearchpeer-review

Synthetic biology and metabolic engineering of actinomycetes for natural product discovery

Palazzotto, E., Tong, Y., Lee, S. Y. & Weber, T., 2019, In : Biotechnology Advances. 37, 6, 107366.

Research output: Contribution to journalJournal articleResearchpeer-review

149 Downloads (Pure)

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

Blin, K., Pascal Andreu, V., de Los Santos, E. L. C., Del Carratore, F., Lee, S. Y., Medema, M. H. & Weber, T., 2019, In : Nucleic acids research. 47, D1, p. D625–D630

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
25 Downloads (Pure)

The Draft Whole-Genome Sequence of the Antibiotic Producer Empedobacter haloabium ATCC 31962 Provides Indications for Its Taxonomic Reclassification

Miess, H., Arlt, P., Apel, A. K., Weber, T., Nieselt, K., Hanssen, F., Czemmel, S., Nahnsen, S. & Gross, H., 2019, In : Microbiology Resource Announcements. 8, 45, 2 p., e01120-19.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
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2018
207 Downloads (Pure)

Filling the Gaps in the Kirromycin Biosynthesis: Deciphering the Role of Genes Involved in Ethylmalonyl-CoA Supply and Tailoring Reactions

Robertsen, H. L., Musiol-Kroll, E. M., Ding, L., Laiple, K. J., Hofeditz, T., Wohlleben, W., Lee, S. Y., Grond, S. & Weber, T., 2018, In : Scientific Reports. 8, 9 p., 3230.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
174 Downloads (Pure)

Lysoquinone-TH1, a New Polyphenolic Tridecaketide Produced by Expressing the Lysolipin Minimal PKS II in Streptomyces albus

Hofeditz, T., Unsin, C. E-M., Wiese, J., Imhoff, J. F., Wohlleben, W., Grond, S. & Weber, T., 2018, In : Antibiotics. 7, 3, p. 53

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
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Omics and multi-omics approaches to study the biosynthesis of secondary metabolites in microorganisms

Palazzotto, E. & Weber, T., 2018, In : Current opinion in Microbiology. 45, p. 109-116

Research output: Contribution to journalJournal articleResearchpeer-review

127 Downloads (Pure)

Patscanui: an intuitive web interface for searching patterns in DNA and protein data

Blin, K., Wohlleben, W. & Weber, T., 2018, In : Nucleic acids research. 46, W1, p. W205-W208

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
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2017
252 Downloads (Pure)

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

Blin, K., Wolf, T., Chevrette, M. G., Lu, X., Schwalen, C. J., Kautsar, S. A., Suarez Duran, H. G., de Los Santos, E. L. C., Kim, H. U., Nave, M., Dickschat, J. S., Mitchell, D. A., Shelest, E., Breitling, R., Takano, E., Lee, S. Y., Weber, T. & Medema, M. H., 2017, In : Nucleic acids research. 45, p. W36-W41

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
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Cyanodermella asteris sp. nov. (Ostropales) from the inflorescence axis of Aster tataricus

Jahn, L., Schafhauser, T., Pan, S., Weber, T., Wohlleben, W., Fewer, D., Sivonen, K., Flor, L., van Pée, K-H., Caradec, T., Jacques, P., Huijbers, M. M. E., van Berkel, W. J. H. & Ludwig-Müller, J., 2017, In : Mycotaxon. 132, p. 107-123

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
232 Downloads (Pure)

Designing sgRNAs with CRISPy web: Tips and tricks of the trade

Blin, K., Lee, S. Y. & Weber, T., 2017, In : Lab Times. 1, p. 53

Research output: Contribution to journalJournal articleResearch

Open Access
File
355 Downloads (Pure)

Dissemination of antibiotic resistance genes from antibiotic producers to pathogens

Jiang, X., Ellabaan, M. M. H., Charusanti, P., Munck, C., Blin, K., Tong, Y., Weber, T., Sommer, M. O. A. & Lee, S. Y., 2017, In : Nature Communications. 8, 15784.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
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Linking secondary metabolites to biosynthesis genes in the fungal endophyte Cyanodermella asteris: The anti-cancer bisanthraquinone skyrin

Jahn, L., Schafhauser, T., Wibberg, D., Rückert, C., Winkler, A., Kulik, A., Weber, T., Flor, L., van Pée, K-H., Kalinowski, J., Ludwig-Müllera, J. & Wohlleben, W., 2017, In : Journal of Biotechnology. 257, p. 233-239

Research output: Contribution to journalJournal articleResearchpeer-review

Recent development of computational resources for new antibiotics discovery

Kim, H. U., Blin, K., Lee, S. Y. & Weber, T., 2017, In : Current opinion in Microbiology. 39, p. 113-120 8 p.

Research output: Contribution to journalJournal articleResearchpeer-review

184 Downloads (Pure)

The Antibiotic Resistant Target Seeker (ARTS), an exploration engine for antibiotic cluster prioritization and novel drug target discovery

Alanjary, M., Kronmiller, B., Adamek, M., Blin, K., Weber, T., Huson, D., Philmus, B. & Ziemert, N., 2017, In : Nucleic acids research. 45, p. W42-W48

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
414 Downloads (Pure)

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

Blin, K., Medema, M. H., Kottmann, R., Lee, S. Y. & Weber, T., 2017, In : Nucleic acids research. 45, D1, p. D555-D559 5 p.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
129 Downloads (Pure)

Towards systems metabolic engineering of streptomycetes for secondary metabolites production

Robertsen, H. L., Weber, T., Kim, H. U. & Lee, S. Y., 2017, In : Biotechnology Journal. 27 p., 1700465.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
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2016
405 Downloads (Pure)

CRISPy-web: An online resource to design sgRNAs for CRISPR applications

Blin, K., Pedersen, L. E., Weber, T. & Lee, S. Y., 2016, In : Synthetic and Systems Biotechnology. 1, 2, p. 118-121 4 p.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
230 Downloads (Pure)

Elucidating the molecular physiology of lantibiotic NAI-107 production in Microbispora ATCC-PTA-5024

Gallo, G., Renzone, G., Palazzotto, E., Monciardini, P., Arena, S., Faddetta, T., Giardina, A., Alduina, R., Weber, T., Sangiorgi, F., Russo, A., Spinelli, G., Sosio, M., Scaloni, A. & Puglia, A. M., 2016, In : B M C Genomics. 17, 42, 17 p.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
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Identification and activation of novel biosynthetic gene clusters by genome mining in the kirromycin producer Streptomyces collinus Tü 365

Iftime, D., Kulik, A., Härtner, T., Rohrer, S., Niedermeyer, T. H. J., Stegmann, E., Weber, T. & Wohlleben, W., 2016, In : Journal of Industrial Microbiology and Biotechnology. 43, 2, p. 277-291 15 p.

Research output: Contribution to journalJournal articleResearchpeer-review

502 Downloads (Pure)

Metabolic engineering with systems biology tools to optimize production of prokaryotic secondary metabolites

Kim, H. U., Charusanti, P., Lee, S. Y. & Weber, T., 2016, In : Natural Product Reports. 33, p. 933-941 9 p.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
270 Downloads (Pure)

The cyclochlorotine mycotoxin is produced by the nonribosomal peptide synthetase CctN in Talaromyces islandicus (“Penicillium islandicum”)

Schafhauser, T., Kirchner, N., Kulik, A., Huijbers, M. M. E., Flor, L., Caradec, T., Fewer, D. P., Gross, H., Jacques, P., Jahn, L., Jokela, J., Leclère, V., Ludwig-Müller, J., Sivonen, K., van Berkel, W. J. H., Weber, T., Wohlleben, W. & van Pée, K-H., 2016, In : Environmental Microbiology. 18, 11, p. 3728–3741

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
1150 Downloads (Pure)

The secondary metabolite bioinformatics portal: Computational tools to facilitate synthetic biology of secondary metabolite production

Weber, T. & Kim, H. U., 2016, In : Synthetic and Systems Biotechnology. 1, 2, p. 69-79 11 p.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
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2015
585 Downloads (Pure)

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

Weber, T., Blin, K., Duddela, S., Krug, D., Kim, H. U., Bruccoleri, R., Lee, S. Y., Fischbach, M. A., Müller, R. & Wohlleben, W., 2015, In : Nucleic acids research. 43, W1, p. W237-W243 7 p.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
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CRISPR-Cas9 Based Engineering of Actinomycetal Genomes

Tong, Y., Charusanti, P., Zhang, L., Weber, T. & Lee, S. Y., 2015, In : A C S Synthetic Biology. 4, 9, p. 1020-1029 10 p.

Research output: Contribution to journalJournal articleResearchpeer-review

1 Downloads (Pure)

Draft genome sequence of Talaromyces islandicus (“Penicillium islandicum”) WF-38-12, a neglected mold with significant biotechnological potential

Schafhauser, T., Wibberg, D., Rückert, C., Winkler, A., Flor, L., van Pée, K-H., Fewer, D. P., Sivonen, K., Jahn, L. & Weber, T., 2015, In : Journal of Biotechnology. 211, p. 101-102 2 p.

Research output: Contribution to journalJournal articleResearchpeer-review

Metabolic engineering of antibiotic factories: New tools for antibiotic production in actinomycetes

Weber, T., Charusanti, P., Musiol-Kroll, E. M., Jiang, X., Tong, Y., Kim, H. U. & Lee, S. Y., 2015, In : Trends in Biotechnology. 33, 1, p. 15-26 12 p.

Research output: Contribution to journalJournal articleResearchpeer-review

Streptocollin, a type IV lanthipeptide produced by Streptomyces collinus Tü 365

Iftime, D., Jasyk, M., Kulik, A., Imhoff, J. F., Stegmann, E., Wohlleben, W., Süssmuth, R. D. & Weber, T., 2015, In : Chembiochem. 16, 18, p. 2615-2623 9 p.

Research output: Contribution to journalJournal articleResearchpeer-review

2014
436 Downloads (Pure)

Biosynthesis of Phenylnannolone A, a Multidrug Resistance Reversal Agent from the Halotolerant Myxobacterium Nannocystis pusilla B150

Bouhired, S. M., Crüsemann, M., Almeida, C., Weber, T., Piel, J., Schäberle, T. F. & König, G. M., 2014, In : ChemBioChem. 15, 5, p. 757-765

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
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Complete genome sequence of the actinobacterium Amycolatopsis japonica MG417-CF17T (=DSM 44213T) producing (S,S)-N,N′-ethylenediaminedisuccinic acid

Stegmann, E., Albersmeier, A., Spohn, M., Gert, H., Weber, T., Wohlleben, W., Kalinowski, J. & Rückert, C., 2014, In : Journal of Biotechnology. 189, p. 46-47

Research output: Contribution to journalJournal articleResearchpeer-review

Draft Genome Sequence of the Microbispora sp. Strain ATCC-PTA-5024, Producing the Lantibiotic NAI-107

Sosio, M., Gallo, G., Pozzi, R., Serina, S., Monciardini, P., Bera, A., Stegmann, E. & Weber, T., 2014, In : Genome Announcements. 2, 1, p. e01198-13

Research output: Contribution to journalJournal articleResearchpeer-review

232 Downloads (Pure)

Improved lanthipeptide detection and prediction for antiSMASH

Blin, K., Kazempour, D., Wohlleben, W. & Weber, T., 2014, In : P L o S One. 9, 2, 7 p., e89420.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
1 Downloads (Pure)

In silico tools for the analysis of antibiotic biosynthetic pathways.

Weber, T., 2014, In : International Journal of Medical Microbiology. 304, p. 230-235

Research output: Contribution to journalJournal articleResearchpeer-review

94 Downloads (Pure)

Novel Amycolatopsis balhimycina biochemical abilities unveiled by proteomics: FEMS Microbiol Lett

Alduina, R., Gallo, G., Renzone, G., Weber, T., Scaloni, A. & Puglia, A. M., 2014, In : F E M S Microbiology Letters. 351, p. 209-215

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
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Reprogramming Acyl Carrier Protein Interactions of an Acyl-CoA Promiscuous trans-Acyltransferase

Ye, Z., Musiol-Kroll, E. M., Weber, T. & Williams, G. J., 2014, In : Chemistry & Biology. 21, p. 636-646

Research output: Contribution to journalJournal articleResearchpeer-review

2013

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

Blin, K., Medema, M. H., Kazempour, D., Fischbach, M., Breitling, R., Takano, E. & Weber, T., 2013, In : Nucleic acids research. 41, W1, p. W204-W212

Research output: Contribution to journalJournal articleResearchpeer-review

Complete genome sequence of the kirromycin producer Streptomyces collinus Tü 365 consisting of a linear chromosome and two linear plasmids

Rückert, C., Szczepanowski, R., Albersmeier, A., Goesmann, A., Iftime, D., Musiol-Kroll, E. M., Blin, K., Wohlleben, W., Pühler, A., Kalinowski, J. & Weber, T., 2013, In : Journal of biotechnology. 168, p. 739-740

Research output: Contribution to journalJournal articleResearchpeer-review

Detection and quantification of a mycorrhization helper bacterium and a mycorrhizal fungus in plant-soil microcosms at different levels of complexity

Kurth, F., Zeitler, K., Feldhahn, L., Neu, T. R., Weber, T., Kristufek, V., Wubet, T., Herrmann, S., Buscot, F. & Tarkka, M. T., 2013, In : B M C Microbiology. 13, p. 205 1 p.

Research output: Contribution to journalJournal articleResearchpeer-review

Poly Specific trans-Acyltransferase Machinery Revealed via Engineered Acyl-CoA Synthetases

Koryakina, I., McArthur, J., Randall, S., Draelos, M. M., Musiol, E. M., Muddiman, D. C., Weber, T. & Williams, G. J., 2013, In : A C S Chemical Biology. 8, p. 200-208 9 p.

Research output: Contribution to journalJournal articleResearchpeer-review

The AT2 domain of KirCI loads malonyl extender units to the ACPs of the kirromycin PKS

Musiol, E-M., Greule, A., Härtner, T., Kulik, A., Wohlleben, W. & Weber, T., 2013, In : ChemBioChem. 14, p. 1343-1352 10 p.

Research output: Contribution to journalJournal articleResearchpeer-review

2012
236 Downloads (Pure)

Genome-scale metabolic representation of Amycolatopsis balhimycina

Vongsangnak, W., Figueiredo, L. F., Förster, J., Weber, T., Thykær, J., Stegmann, E., Wohlleben, W. & Nielsen, J., 2012, In : Biotechnology and Bioengineering (Print). 109, 7, p. 1798-1807

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
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Synthetic biology of secondary metabolite biosynthesis in actinomycetes: Engineering precursor supply as a way to optimize antibiotic production

Wohlleben, W., Mast, Y., Muth, G., Röttgen, M., Stegmann, E. & Weber, T., 2012, In : F E B S Letters. 586, p. 2171-2176 6 p.

Research output: Contribution to journalJournal articleResearchpeer-review

2011

antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences: Nucleic Acids Research

Medema, M. H., Blin, K., Cimermancic, P., de Jager, V., Zakrzewski, P., Fischbach, M. A., Weber, T., Takano, E. & Breitling, R., 2011, In : Nucleic acids research. 39, p. W339-W346

Research output: Contribution to journalJournal articleResearchpeer-review