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Research Output

2020

Complete Genome Sequences of 13 Bacillus subtilis Soil Isolates for Studying Secondary Metabolite Diversity

Kiesewalter, H. T., Lozano-Andrade, C. N., Maróti, G., Snyder, D., Snyder, D., Jørgensen, T. S., Weber, T. & Kovács, Á. T., 2020, In : Microbiology Resource Announcements. 9, 2, 3 p., e01406-19.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
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8 Downloads (Pure)

Genome Mining Approaches to Bacterial Natural Product Discovery

Ziemert, N., Weber, T. & Medema, M. H., 2020, (Accepted/In press) In : Reference Module in Chemistry, Molecular Sciences and Chemical Engineering. 15 p.

Research output: Contribution to journalJournal articleResearchpeer-review

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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9 Downloads (Pure)
2019

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

Open Access
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118 Downloads (Pure)

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

CRISPR/Cas-based genome engineering in natural product discovery

Tong, Y., Weber, T. & Lee, S. Y., 2019, In : Natural Product Reports. 36, 9, p. 1225-1372

Research output: Contribution to journalReviewResearchpeer-review

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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108 Downloads (Pure)

Engineering of cell factories for the production of natural products

Weber, T., 2019, In : Natural Product Reports. 36, 9, p. 1231-1232

Research output: Contribution to journalEditorialResearchpeer-review

Genome-Scale Metabolic Reconstruction of Actinomycetes for Antibiotics Production

Mohite, O. S., Weber, T., Kim, H. U. & Lee, S. Y., 2019, In : Biotechnology Journal. 14, 1, 9 p., 1800377.

Research output: Contribution to journalReviewResearchpeer-review

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
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57 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

Open Access
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251 Downloads (Pure)

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

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
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156 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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34 Downloads (Pure)
2018

CRISPR-Cas9 Toolkit for Actinomycete Genome Editing

Tong, Y., Robertsen, H. L., Blin, K., Weber, T. & Lee, S. Y., 2018, Synthetic Metabolic Pathways. Vol. 1671. p. 163-184 (Methods in Molecular Biology).

Research output: Chapter in Book/Report/Conference proceedingBook chapterResearchpeer-review

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
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214 Downloads (Pure)

Immense diversity found in secondary metabolite gene clusters in filamentous fungi and bacteria using comparative genomics

Vesth, T., Frisvad, J., Kovács, Á., Jelsbak, L., Weber, T., Baker, S. E. & Andersen, M. R., 2018. 1 p.

Research output: Contribution to conferencePosterResearchpeer-review

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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184 Downloads (Pure)

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

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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133 Downloads (Pure)
2017

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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258 Downloads (Pure)

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

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
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236 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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365 Downloads (Pure)

Filling The Gaps In The Kirromycin Biosynthetic Gene Cluster In Streptomyces Collinus Tü 365

Robertsen, H. L., Musiol-Kroll, E. M., Ding, L., Lee, S. Y. & Weber, T., 2017.

Research output: Contribution to conferenceConference abstract for conferenceResearchpeer-review

Open Access
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62 Downloads (Pure)

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

Polyketide Bioderivatization Using the Promiscuous Acyltransferase KirCII

Musiol-Kroll, E. M., Zubeil, F., Schafhauser, T., Härtner, T., Kulik, A., McArthur, J., Koryakina, I., Wohlleben, W., Grond, S., Williams, G. J., Lee, S. Y. & Weber, T., 2017, In : A C S Synthetic Biology. 6, 3, p. 421-427

Research output: Contribution to journalLetterResearchpeer-review

Open Access
1 Downloads (Pure)

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

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
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188 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

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423 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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136 Downloads (Pure)
2016

Bioinformatics Tools for the Discovery of New Nonribosomal Peptides

Leclère, V., Weber, T., Jacques, P. & Pupin, M., 2016, Nonribosomal Peptide and Polyketide Biosynthesis: Methods and Protocols. Springer, Vol. 1401. p. 209-232 24 p. (Methods in Molecular Biology).

Research output: Chapter in Book/Report/Conference proceedingBook chapterResearchpeer-review

CRISPR/CAS9 based engineering of actinomycetal genomes

Weber, T., Tong, Y. & Lee, S. Y., 29 Sep 2016, IPC No. C12N 15/ 90 A I, Patent No. WO2016150855, 29 Sep 2016, Priority date 20 Mar 2015, Priority No. EP20150160126

Research output: Patent

Open Access
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303 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
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417 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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235 Downloads (Pure)

Engineering of actinomycetes using CRISPR/Cas9 technologies

Weber, T., Tong, Y., Blin, K. & Lee, S. Y., 2016, In : Planta Medica. 81, S01, 1 p.

Research output: Contribution to journalConference abstract in journalResearchpeer-review

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

Introduction to the Special Issue “Bioinformatic tools and approaches for Synthetic Biology of natural products”

Weber, T., 2016, In : Synthetic and Systems Biotechnology. 1, 2, p. 67-68 2 p.

Research output: Contribution to journalEditorialResearchpeer-review

Open Access
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352 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
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510 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
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279 Downloads (Pure)

The evolution of genome mining in microbes – a review

Ziemert, N., Alanjary, M. & Weber, T., 2016, In : Natural Product Reports. 33, p. 988-1005 18 p.

Research output: Contribution to journalReviewResearchpeer-review

Open Access
File
705 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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1190 Downloads (Pure)
2015

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
File
594 Downloads (Pure)

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

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

1 Downloads (Pure)

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

Minimum Information about a Biosynthetic Gene cluster

Medema, M. H., Kottmann, R., Yilmaz, P., Cummings, M., Biggins, J. B., Blin, K., de Bruijn, I., Kim, H. U., Nielsen, J. & Weber, T., 2015, In : Nature Chemical Biology. 11, 9, p. 625-631 7 p.

Research output: Contribution to journalComment/debateResearchpeer-review

Open Access
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301 Downloads (Pure)

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