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., and Weber, T. (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:10.1038/s41598-021-97571-2
23. 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
24. 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
25. 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
26. 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
27. 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
28. 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
29. Genilloud, O. (2019). Natural products discovery and potential for new antibiotics. Curr Opin Microbiol. DOI:10.1016/j.mib.2019.10.012
30. Kat Steinke, Omkar S. Mohite, Tilmann Weber, Ákos T. Kovács. Phylogenetic Distribution of Secondary Metabolites in the Bacillus subtilis Species Complex. ASM Journals, DOI: 10.1128/mSystems.00057-21.
31. Heiko T. Kiesewalter, Carlos N. Lozano-Andrade, Mario Wibowo, Mikael L. Strube, Gergely Maróti, Dan Snyder, Tue Sparholt Jørgensen, Thomas O. Larsen, Vaughn S. Cooper, Tilmann Weber, Ákos T. Kovács. Genomic and Chemical Diversity of Bacillus subtilis Secondary Metabolites against Plant Pathogenic Fungi. ASM Journals, DOI: 10.1128/mSystems.00770-20.
32. Román-Hurtado F, Sánchez-Hidalgo M, Martín J, Ortiz-López FJ, Carretero-Molina D, Reyes F, Genilloud O. One Pathway, Two Cyclic Non-Ribosomal Pentapeptides: Heterologous Expression of BE-18257 Antibiotics and Pentaminomycins from Streptomyces cacaoi CA-170360. Microorganisms, DOI: 10.3390/microorganisms9010135.
33. Carretero-Molina, Daniel; Ortiz-López, Francisco Javier; Martin, Jesus; González, Ignacio; Sánchez-Hidalgo, Marina; Román-Hurtado, Fernando; Díaz Navarro, Caridad; de la Cruz, Mercedes; Genilloud, Olga; Reyes, Fernando. Pentaminomycins F and G, First Non-Ribosomal Peptides Containing 2-Pyridylalanine.
34. Beck, C., Garzón, J.F.G., and Weber, T. (2020). Recent Advances in Re-engineering Modular PKS and NRPS Assembly Lines. Biotechnology and Bioprocess Engineering 25, 886-894.
35. Dongsoo Yang, Woo Dae Jang, and Sang Yup Lee. Production of Carminic Acid by Metabolically Engineered Escherichia coli. ACS Publications.
36. Mohammad Rifqi Ghiffary, Cindy Pricilia Surya Prabowo, Komal Sharma, Yuchun Yan, Sang Yup Lee and Hyun Uk Kim. High-Level Production of the Natural Blue Pigment Indigoidine from Metabolically Engineered Corynebacterium glutamicum for Sustainable Fabric Dyes. ACS Publications.
37. Mungan MD, Blin K, Ziemert N. ARTS-DB: a database for antibiotic resistant targets. Nucleic Acids Res. 2022;50(D1):D736-D40. DOI: 10.1093/nar/gkab940.
38. Christopher M. Whitford, Pablo Cruz-Morales, Jay D. Keasling, and Tilmann Weber. The Design-Build-Test-Learn cycle for metabolic engineering of Streptomycetes. Essays Biochem (2021).
39. Charlotte Beck, Tetiana Gren, Tue S Jørgensen, Ignacio González, Fernando Román-Hurtado, Daniel Oves-Costales, Olga Genilloud, Tilmann Weber. Complete Genome Sequence of Streptomyces sp. Strain CA-256286.
40. Kai Blin, Simon Shaw, Alexander M Kloosterman, Zach Charlop-Powers, Gilles P van Wezel, Marnix H Medema, Tilmann Weber. antiSMASH 6.0: improving cluster detection and comparison capabilities. Nucleic Acids Res. DOI:10.1093/nar/gkab335
41. Erik Mingyar, Lucas Mühling, Andreas Kulik, Anika Winkler, Daniel Wibberg, Jörn Kalinowski, Kai Blin, Tilmann Weber, Wolfgang Wohlleben and Evi Stegmann. A Regulator Based “Semi-Targeted” Approach to Activate Silent Biosynthetic Gene Clusters. Int. J. Mol. Sci. 2021. DOI:10.3390/ijms22147567
42. Tue S. Jørgensen, Tetiana Gren, Eftychia E. Kontou, Ignacio González, Fernando Román-Hurtado, Daniel Oves-Costales, Emil Thomsen, Pep Charusanti, Olga Genilloud and Tilmann Weber. Complete Genome Sequence of the Rare Actinobacterium Kutzneria sp. Strain CA-103260. Microb. Res. Announc. 2021. DOI:10.1128/MRA.00499-21
43. Eftychia E. Kontou, Tetiana Gren, Francisco Javier Ortiz-López, Emil Thomsen, Daniel Oves-Costales, Caridad Díaz, Mercedes de la Cruz, Xinglin Jiang, Tue S. Jørgensen, Kai Blin, Pep Charusanti, Fernando Reyes, Olga Genilloud and Tilmann Weber. Discovery and Characterization of Epemicins A and B, New 30-Membered Macrolides from Kutzneria sp. CA-103260. ACS Chem. Biol. 2021. DOI:10.1021/acschembio.1c00318
44. Marcus Miethke, Marco Pieroni, Tilmann Weber et al. Towards the sustainable discovery and development of new antibiotics. Nature Reviews Chemistry (2021). DOI:10.1038/s41570-021-00313-1
45. Yaojun Tong, Tue S. Jørgensen, Christopher M. Whitford, Tilmann Weber, Sang Yup Lee. A versatile genetic engineering toolkit for E. coli based on CRISPR-prime editing. Nature Communications (2021). DOI:10.1038/s41467-021-25541-3
46. Daniel Carretero-Molina, Francisco Javier Ortiz-López, Tetiana Gren, Daniel Oves-Costales, Jesús Martín, Fernando Román-Hurtado, Tue Sparholt Jørgensen, Mercedes de la Cruz, Caridad Díaz, Francisca Vicente, Kai Blin, Fernando Reyes, Tilmann Weber, Olga Genilloud. Identification of the 216kbp gene cluster and structure elucidation of gargantulides B and C, new complex 52-membered macrolides from Amycolatopsis sp. BioRxiv (2021). DOI:10.1101/2021.08.11.455926
47. Beck C, Gren T, Ortiz-López FJ, Jørgensen TS, Carretero-Molina D, Martín Serrano J, et al. Activation and Identification of a Griseusin Cluster in Streptomyces sp. CA-256286 by Employing Transcriptional Regulators and Multi-Omics Methods. Molecules. 2021;26(21):6580. DOI: 10.3390/molecules26216580.
48. Schmid JC, Frey K, Scheiner M, Garzon JFG, Stafforst L, Fricke JN, et al. The structure of cyclodecatriene collinolactone, its biosynthesis and semisynthetic analogues: Effects of monoastral phenotype and protection from intracellular oxidative stress. Angew Chem Int Ed Engl. (2021);60(43):23212-6. DOI: 10.1002/anie.202106802.
49. Daniel Carretero-Molina, Francisco Javier Ortiz-López, Tetiana Gren, Daniel Oves-Costales, Jesús Martín, Fernando Román-Hurtado, Tue Sparholt Jørgensen, Mercedes de la Cruz, Caridad Diaz, Francisca Vicente, Kai Blin, Fernando Reyes, Tilmann Weber and Olga Genilloud. Discovery of gargantulides B and C, new 52-membered macrolactones from Amycolatopsis sp. Complete absolute stereochemistry of the gargantulide family. Organic Chemistry Frontiers (2022). DOI:10.1039/D1QO01480C.
50. Sanchéz-Navarro R, Nuhamunada M, Mohite OS, Wasmund K, Albertsen M, Gram L, et al. Long-Read Metagenome-Assembled Genomes Improve Identification of Novel Complete Biosynthetic Gene Clusters in a Complex Microbial Activated Sludge Ecosystem. mSystems. (2022) 2022:e0063222. DOI: 10.1128/msystems.00632-22.
51. Jørgensen TS, Pedersen MS, Blin K, Kuntke F, Salling HK, Marvig RL, et al. SpikeSeq: A rapid, cost efficient and simple method to identify SARS-CoV-2 variants of concern by Sanger sequencing part of the spike protein gene. J Virol Methods. 2022;312:114648. DOI: 10.1016/j.jviromet.2022.114648.
52. Ghiffary MR, Prabowo CPS, Adidjaja JJ, Lee SY, Kim HU. Systems metabolic engineering of Corynebacterium glutamicum for the efficient production of beta-alanine. Metab Eng. 2022;74:121-9. DOI: 10.1016/j.ymben.2022.10.009.
53. Kontou EE, Walter A, Alka O, Pfeuffer J, Sachsenberg T, Mohite O, et al. UmetaFlow: An untargeted metabolomics workflow for high-throughput data processing and analysis. ChemRxiv (PREPRINT). 2022:DOI: 10.26434/chemrxiv-2022-z0t4g-v2.
54. Nielsen JB, Gren T, Mohite OS, Jorgensen TS, Klitgaard AK, Mourched AS, et al. Identification of the Biosynthetic Gene Cluster for Pyracrimycin A, an Antibiotic Produced by Streptomyces sp. ACS Chem Biol. 2022;17(9):2411-7. DOI: 10.1021/acschembio.2c00480.
55. Jarmusch AK, Aron AT, Petras D, Phelan VV, Bittremieux W, Acharya DD, et al. A Universal Language for Finding Mass Spectrometry Data Patterns. bioRxiv (PREPRINT). 2022. DOI: 10.1101/2022.08.06.503000.
56. Sterndorff EB, Jorgensen TS, Garzon JFG, Schmid J, Grond S, Weber T. Complete Genome Sequence of the Collinolactone Producer Streptomyces sp. Strain Go40/10. Microbiol Resour Announc. 2022;11(8):e0022022. DOI: 10.1128/mra.00220-22.
57. Mohite OS, Lloyd CJ, Monk JM, Weber T, Palsson BO. Pangenome analysis of Enterobacteria reveals richness of secondary metabolite gene clusters and their associated gene sets. Synth Syst Biotechnol. 2022;7(3):900-10. DOI: 10.1016/j.synbio.2022.04.011.