PUBLICATIONS RELATED TO THE IIMENA PROJECT:
1. Palazzotto, E., and Weber, T. (2018). Omics and multi-omics approaches to study the biosynthesis of secondary metabolites in microorganisms. Curr Opin Microbiol. 45:109-116. DOI: 10.1016/j.mib.2018.03.004
2. Kai Blin, Wolfgang Wohlleben, Tilmann Weber. (2018). Patscanui: an intuitive web interface for searching patterns in DNA and Protein data. Nucleic Acids Research 46: W2015-W208. DOI: https://doi.org/10.1093/nar/gky321
3. Blin, K., Pascal Andreu, V., de los Santos, E.L., Del Carratore, F., Lee, S.Y., Medema, M.H., and Weber, T. (2018). The antiSMASH Database Version 2 – A Comprehensive Resource on Secondary Metabolite Biosynthetic Gene Clusters. Nucleic Acids Res, DOI: 10.1093/nar/gky1060.
4. Kyeong RokChoi, Jae SungCho, In JinCho, DahyeonPark, Sang YupLee. (2018). Markerless gene knockout and integration to express heterologous biosynthetic gene clusters in Pseudomonas putida. Metabolic Engineering 47: 463-474. DOI: https://doi.org/10.1016/j.ymben.2018.05.003
5. Omkar S. Mohite, Tilmann Weber, Hyun Uk Kim, Sang Yup Lee (2018). Genome-Scale Metabolic Reconstruction of Actinomycetes for Antibiotics Production. Biotechnology J. DOI: 10.1002/biot.201800377
6. , , , , , , and Repurposing type III polyketide synthase as a malonyl-CoA biosensor for metabolic engineering in bacteria. PNAS. DOI: 10.1073/pnas.1808567115
7. Blin, K., Kim, H.U., Medema, M.H., and Weber, T. (2017). Recent development of antiSMASH and other computational approaches to mine secondary metabolite biosynthetic gene clusters. Brief Bioinform, DOI: 10.1093/bib/bbx1146.
8. Kai Blin, Thomas Wolf, Marc G. Chevrette, Xiaowen Lu, Christopher J. Schwalen, Satria A. Kautsar, Hernando G. Suarez Duran, Emmanuel L. C. de los Santos, Hyun Uk Kim, Mariana Nave, Jeroen S. Dickschat, Douglas A. Mitchell, Ekaterina Shelest, Rainer Breitling, Eriko Takano, Sang Yup Lee, Tilmann Weber, Marnix H. Medema. . antiSMASH 4.0—improvements in chemistry prediction and gene cluster boundary identification. Nucleic Acids Research DOI: 10.1093/nar/gkx319
9. Xinglin Jiang, Mostafa M. Hashim Ellabaan, Pep Charusanti, Christian Munck, Kai Blin, Yaojun Tong, Tilmann Weber, Morten O. A. Sommer & Sang Yup Lee. . Dissemination of antibiotic resistance genes from antibiotic producers to pathogens. Nature Communications DOI:10.1038/ncomms15784
10. Helene Lunde Robertsen, Tilmann Weber, Hyun Uk Kim, Sang Yup Lee. Toward Systems Metabolic Engineering of Streptomycetes for Secondary Metabolites Production. Biotechnology Journal DOI: 10.1002/biot.201700465
11. Villebro R, Shaw S, Blin K, Weber T. Sequence-based classification of type II polyketide synthase biosynthetic gene clusters for antiSMASH. Journal of Industrial Microbiology and Biotechnology. DOI: 10.1007/s10295-018-02131-9
12. Palazzotto E, Tong Y, Lee SY, Weber T. Synthetic biology and metabolic engineering of actinomycetes for natural product discovery. Biotechnology Advanced. DOI: 10.1016-j.biotechhadv.2019.03.005
14. Kai Blin, Simon Shaw, Katharina Steinke, Rasmus Villebro, Nadine Ziemert, Sang Yup Lee, Marnix H Medema, Tilmann Weber. antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline. Nucleic Acids Research. DOI:10.1093/nar/gkz310
15. Omkar S. Mohite, Colton J. Lloyd, Jonathan M. Monk, Tilmann Weber and Bernhard O. Palsson. Pangenome Analysis of Enterobacteria Reveals Richness of Secondary Metabolite Gene Clusters and their Associated Gene Sets. bioRxiv. DOI:10.1101/781328
16. Yaojun Tong, Christopher M. Whitford, Helene L. Robertsen, Kai Blin, Tue S. Jørgensen, Andreas K. Klitgaard, Tetiana Gren, Xinglin Jiang, Tilmann Weber and Sang Yup Lee. Highly efficient DSB-free base editing for streptomycetes with CRISPR-BEST. Proceedings of the National Academy of Sciences U.S.A. DOI:10.1073/pnas.1913493116
17. Satria A Kautsar, Kai Blin, Simon Shaw, Jorge C Navarro-Muñoz, Barbara R Terlouw, Justin J J van der Hooft, Jeffrey A van Santen, Vittorio Tracanna, Hernando G Suarez Duran, Victòria Pascal Andreu, Nelly Selem-Mojica, Mohammad Alanjary, Serina L Robinson, George Lund, Samuel C Epstein, Ashley C Sisto, Louise K Charkoudian, Jérôme Collemare, Roger G Linington, Tilmann Weber, Marnix H Medema. MIBiG 2.0: a repository for biosynthetic gene clusters of known funktion. Nucleic Acids Research. DOI:10.1093/nar/gkz882
18. Mehmet Direnç Mungan, Mohammad Alanjary, Kai Blin, Tilmann Weber, Marnix H Medema, Nadine Ziemert. ARTS 2.0: feature updates and expansion of the Antibiotic Resistant Target Seeker for comparative genome mining. Nucleic Acids Research. DOI:10.1093/nar/gkaa374
19. Yaojun Tong, Christopher M. Whitford, Kai Blin, Tue S. Jørgensen, Tilmann Weber, and Sang Yup Lee (2020). CRISPR-Cas9, CRISPRi and CRISPR-BEST-mediated genetic manipulation in streptomycetes. Nature Protocols. DOI:10.1038/s41596-020-0339-z