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. Dongsoo Yang, Won Jun Kim, Seung Min Yoo, Jong Hyun Choi, Shin Hee Ha, Mun Hee Lee, and Sang Yup Lee (2018). 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

13. Choi KR, Lee SY. Protocols for RecET‐based markerless gene knockout and integration to express heterologous biosynthetic gene clusters in Pseudomonas putida. Microbial Biotechnology. DOI: 10.1111/1751-7915.13374

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. 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

18. 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

19. Jiang, X., Palazzotto, E., Wybraniec, E., Munro, L.J., Zhang, H., Kell, D.B., Weber, T., and Lee, S.Y. (2020). Automating Cloning by Natural Transformation. ACS Synth Biol. DOI:10.1021/acssynbio.0c00240

20. Blin, K., Shaw, S., Kautsar, S.A., Medema, M.H., and Weber, T. (2020). The antiSMASH database version 3 – increased taxonomic coverage and new query features for modular enzymes. Nucleic Acids Res. DOI:10.1093/nar/gkaa978

21. Gren, T., Jørgensen, T.S., Whitford, C.M., Weber, T., and Dunning Hotopp, J.C. (2020). High-Quality Sequencing, Assembly, and Annotation of the Streptomyces griseofuscus DSM 40191 Genome. Microbiology Resource Announcements. DOI:10.1128/mra.01100-20

22. Gren, T., Whitford, C.M., Mohite, O.S., Jørgensen, T.S., Kontou, E.E., Nielsen, J.B., Lee, S.Y., and Weber, T. (2020). Characterization and Engineering of Streptomyces griseofuscus DSM 40191 as a Potential Host for Heterologous Expression of Biosynthetic Gene Clusters. DOI:10.1101/2020.11.06.372458

23. Steinke, K., Mohite, O.S., Weber, T., and Kovács, Á.T. (2020). Phylogenetic distribution of secondary metabolites in the Bacillus subtilis species complex. DOI:10.1101/2020.10.28.358507

24. Kautsar, S.A., Blin, K., Shaw, S., Weber, T., and Medema, M.H. (2020). BiG-FAM: the biosynthetic gene cluster families database. Nucleic Acids Res. DOI:10.1093/nar/gkaa812

25. Yang, D., Park, S.Y., Park, Y.S., Eun, H., and Lee, S.Y. (2020). Metabolic Engineering of Escherichia coli for Natural Product Biosynthesis. Trends Biotechnol. DOI:10.1016/j.tibtech.2019.11.007

26. Tong, Y., Jørgensen, T.S., Whitford, C.M., Weber, T., and Lee, S.Y. (2020). CRISPR-nRAGE, a Cas9 nickase-reverse transcriptase assisted versatile genetic engineering toolkit for E. coli. DOI:10.1101/2020.09.02.279141

27. Kautsar, S.A., Blin, K., Shaw, S., Navarro-Munoz, 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., and Medema, M.H. (2020). MIBiG 2.0: a repository for biosynthetic gene clusters of known function. Nucleic Acids Res. DOI:10.1093/nar/gkz882

28. Blin, K., Shaw, S., Tong, Y., and Weber, T. (2020). Designing sgRNAs for CRISPR-BEST base editing applications with CRISPy-web 2.0. Synth Syst Biotechnol. DOI:10.1016/j.synbio.2020.05.005

29. Tong, Y., and Deng, Z. (2020). An aurora of natural products-based drug discovery is coming. Synth Syst Biotechnol. DOI:10.1016/j.synbio.2020.05.003

30. Genilloud, O. (2019). Natural products discovery and potential for new antibiotics. Curr Opin Microbiol. DOI:10.1016/j.mib.2019.10.012