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2019
 

A comprehensive metabolic map for production of bio-based chemicals

Lee, Sang Yup ; Kim, Hyun Uk ; Chae, Tong Un ; Cho, Jae Sung ; Kim, Je Woong ; Shin, Jae Ho ; Kim, Dong In ; Ko, Yoo Sung ; Jang, Woo Dae ; Jang, Yu Sin
in: Nature Catalysis, vol: 2, issue: 1, pages: 18-33

Type: Review (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1038/s41929-018-0212-4

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antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline

Blin, Kai ; Shaw, Simon ; Steinke, Katharina ; Villebro, Rasmus ; Ziemert, Nadine ; Lee, Sang Yup ; Medema, Marnix H ; Weber, Tilmann
in: Nucleic acids research, vol: 87, issue: W2, pages: W81-W87

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1093/nar/gkz310

 

Are we there yet? How and when specific biotechnologies will improve human health

O'Day, Elizabeth ; Hosta-Rigau, Leticia ; Oyarzún, Diego A. ; Okano, Hideyuki ; de Lorenzo, Víctor ; von Kameke, Conrad ; Alsafar, Habiba ; Cao, Cong ; Chen, Guo-Qiang ; Ji, Weizhi ; Roberts, Richard J. ; Ronaghi, Mostafa ; Yeung, Karen ; Zhang, Feng ; Lee, Sang Yup
in: Biotechnology Journal, vol: 14, issue: 1, pages: 11

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1002/biot.201800195

 

Birch sap as a novel treatment for birch pollen allergy

Sancho Vega, Ana Isabel ; Hornslet, Sofie Emilie ; Rønne, T. ; Lindholm Bøgh, Katrine
in: Allergy: European Journal of Allergy and Clinical Immunology, vol: 74, issue: Suppl. 106, pages: 695
Presented at:
EAACI 2019

Type: Conference abstract in journal (Peer reviewed)

Status: Published     |    Year: 2019

 

CRISPR/Cas-based genome engineering in natural product discovery

Tong, Yaojun ; Weber, Tilmann ; Lee, Sang Yup
in: Natural Product Reports, vol: 36, issue: 9, pages: 1225-1372

Type: Review (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1039/C8NP00089A

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

Devi, Sagarika ; Kiesewalter, Heiko T. ; Kovács, Renátó ; Frisvad, Jens Christian ; Weber, Tilmann ; Larsen, Thomas Ostenfeld ; Kovács, Ákos T. ; Ding, Ling
in: Synthetic and Systems Biotechnology, vol: 4, issue: 3, pages: 142-149

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1016/j.synbio.2019.08.002

 

Engineering of cell factories for the production of natural products

Weber, Tilmann
in: Natural Product Reports, vol: 36, issue: 9, pages: 1231-1232

Type: Editorial (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1039/c9np90036e

 

Genome-Scale Metabolic Reconstruction of Actinomycetes for Antibiotics Production

Mohite, Omkar Satyavan ; Weber, Tilmann ; Kim, Hyun Uk ; Lee, Sang Yup
in: Biotechnology Journal, vol: 14, issue: 1

Type: Review (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1002/biot.201800377

 

Protocols for RecET-based markerless gene knockout and integration to express heterologous biosynthetic gene clusters in Pseudomonas putida

Choi, Kyeong Rok ; Lee, Sang Yup
in: Microbial Biotechnology

Type: Journal article (Peer reviewed)

Status: Accepted/In press     |    Year: 2019     |    DOI: https://doi.org/10.1111/1751-7915.13374

 

Recent advances of metabolic engineering strategies in natural isoprenoid production using cell factories

Li, Meijie ; Hou, Feifei ; Wu, Tong ; Jiang, Xinglin ; Li, Fuli ; Liu, Haobao ; Xian, Mo ; Zhang, Haibo
in: Natural Product Reports

Type: Journal article (Peer reviewed)

Status: Accepted/In press     |    Year: 2019     |    DOI: https://doi.org/10.1039/c9np00016j

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

Blin, Kai ; Kim, Hyun Uk ; Medema, Marnix H. ; Weber, Tilmann
in: Briefings in Bioinformatics, vol: 20, issue: 4, pages: 1103-1113

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1093/bib/bbx146

 

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

Villebro, Rasmus ; Shaw, Simon ; Blin, Kai ; Weber, Tilmann
in: Journal of Industrial Microbiology and Biotechnology, vol: 46, issue: 3-4, pages: 469-475

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1007/s10295-018-02131-9

 

Synthetic biology and metabolic engineering of actinomycetes for natural product discovery

Palazzotto, Emilia ; Tong, Yaojun ; Lee, Sang Yup ; Weber, Tilmann
in: Biotechnology Advances, vol: 37, issue: 6

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1016/j.biotechadv.2019.03.005

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

Blin, Kai ; Pascal Andreu, Victòria ; de Los Santos, Emmanuel L C ; Del Carratore, Francesco ; Lee, Sang Yup ; Medema, Marnix H. ; Weber, Tilmann
in: Nucleic acids research, vol: 47, issue: D1, pages: D625–D630

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1093/nar/gky1060

2018
 

Bioconda: sustainable and comprehensive software distribution for the life sciences

Grüning , Björn ; Dale, Ryan ; Sjödin, Andreas ; Chapman, Brad A. ; Rowe, Jillian ; Tomkins-Tinch, Christopher H. ; Valieris, Renan ; Köster, Johannes ; Blin, Kai ; Haudgaard, Mathias ; Kratz, Arne ; Junge, Alexander ; Knudsen, Michael
in: Nature Methods, vol: 15, pages: 475-476

Type: Comment/debate (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1038/s41592-018-0046-7

 

CRISPR-Cas9 Toolkit for Actinomycete Genome Editing

Tong, Yaojun ; Robertsen, Helene Lunde ; Blin, Kai ; Weber, Tilmann ; Lee, Sang Yup
part of: Synthetic Metabolic Pathways, pages: 163-184, 2018

Type: Book chapter (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1007/978-1-4939-7295-1_11

 

Evolution of the Metabolic Engineering Community

Nielsen, Jens ; Lee, Sang Yup
in: Metabolic Engineering, vol: 48, pages: A1-A2

Type: Journal article

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1016/j.ymben.2018.07.014

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

Robertsen, Helene L. ; Musiol-Kroll, Ewa M. ; Ding, Ling ; Laiple, Kristina J. ; Hofeditz, Torben ; Wohlleben, Wolfgang ; Lee, Sang Yup ; Grond, Stephanie ; Weber, Tilmann
in: Scientific Reports, vol: 8

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1038/s41598-018-21507-6

 

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

Vesth, Tammi ; Frisvad, Jens ; Kovács, Ákos ; Jelsbak, Lars ; Weber, Tilmann ; Baker, Scott E. ; Andersen, Mikael R.
Presented at:
17th European Conference on Computational Biology

Type: Poster (Peer reviewed)

Status: Published     |    Year: 2018

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

Hofeditz, Torben ; Unsin, Claudia Eva-Maria ; Wiese, Jutta ; Imhoff, Johannes F. ; Wohlleben, Wolfgang ; Grond, Stephanie ; Weber, Tilmann
in: Antibiotics, vol: 7, issue: 3, pages: 53

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.3390/antibiotics7030053

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Markerless gene knockout and integration to express heterologous biosynthetic gene clusters in Pseudomonas putida

Choi, Kyeong Rok ; Cho, Jae Sung ; Cho, In Jin ; Park, Dahyeon ; Lee, Sang Yup
in: Metabolic Engineering, vol: 47, pages: 463-474

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1016/j.ymben.2018.05.003

 

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

Palazzotto, Emilia ; Weber, Tilmann
in: Current opinion in Microbiology, vol: 45, pages: 109-116

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1016/j.mib.2018.03.004

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

Blin, Kai ; Wohlleben, Wolfgang ; Weber, Tilmann
in: Nucleic acids research, vol: 46, issue: W1, pages: W205-W208

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1093/nar/gky321

 

Repurposing type III polyketide synthase as a malonyl-CoA biosensor for metabolic engineering in bacteria

Yang, Dongsoo ; Kim, Won Jun ; Yoo, Seung Min ; Choi, Jong Hyun ; Ha, Shin Hee ; Lee, Mun Hee ; Lee, Sang Yup
in: Proceedings of the National Academy of Sciences of the United States of America, vol: 115, issue: 40, pages: 9835-9844

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1073/pnas.1808567115

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The power of synthetic biology for bioproduction, remediation and pollution control

de Lorenzo, Víctor ; Prather, Kristala L.J. ; Chen, Guo-Qiang ; O'Day, Elizabeth ; von Kameke, Conrad ; Oyarzún, Diego A. ; Hosta-Rigau, Leticia ; Alsafar, Habiba ; Cao, Cong ; Ji, Weizhi ; Okano, Hideyuki ; Roberts, Richard J. ; Ronaghi, Mostafa ; Yeung, Karen ; Zhang, Feng ; Lee, Sang Yup
in: E M B O Reports, vol: 19, issue: 4

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.15252/embr.201745658

2017
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antiSMASH 4.0-improvements in chemistry prediction and gene cluster boundary identification

Blin, Kai ; Wolf, Thomas ; Chevrette, Marc G. ; Lu, Xiaowen ; Schwalen, Christopher J. ; Kautsar, Satria A. ; Suarez Duran, Hernando G. ; de Los Santos, Emmanuel L. C. ; Kim, Hyun Uk ; Nave, Mariana ; Dickschat, Jeroen S. ; Mitchell, Douglas A. ; Shelest, Ekaterina ; Breitling, Rainer ; Takano, Eriko ; Lee, Sang Yup ; Weber, Tilmann ; Medema, Marnix H.
in: Nucleic acids research, vol: 45, pages: W36-W41

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2017     |    DOI: https://doi.org/10.1093/nar/gkx319

 

Current state and applications of microbial genome-scale metabolic models

Kim, Won Jun ; Kim, Hyun Uk ; Lee, Sang Yup
in: Current Opinion in Systems Biology, vol: 2, pages: 10-18

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2017     |    DOI: https://doi.org/10.1016/j.coisb.2017.03.001

 

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

Jahn, Linda ; Schafhauser, Thomas ; Pan, Stefan ; Weber, Tilmann ; Wohlleben, Wolfgang ; Fewer, David ; Sivonen, Kaarina ; Flor, Liane ; van Pée, Karl-Heinz ; Caradec, Thibault ; Jacques, Philippe ; Huijbers, Mieke M.E. ; van Berkel, Willem J.H. ; Ludwig-Müller, Jutta
in: Mycotaxon, vol: 132, pages: 107-123

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2017     |    DOI: https://doi.org/10.5248/132.107

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Designing sgRNAs with CRISPy web

Blin, Kai ; Lee, Sang Yup ; Weber, Tilmann
in: Lab Times, issue: 1, pages: 53

Type: Journal article

Status: Published     |    Year: 2017

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

Robertsen, Helene Lunde ; Musiol-Kroll, Ewa Maria ; Ding, Ling ; Lee, Sang Yup ; Weber, Tilmann
Presented at:
18th International Symposium on the Biology of Actinomycetes

Type: Conference abstract for conference (Peer reviewed)

Status: Published     |    Year: 2017

 

Framework and resource for more than 11,000 gene-transcript-protein-reaction associations in human metabolism

Ryu, Jae Yong ; Kim, Hyun Uk ; Lee, Sang Yup
in: Proceedings of the National Academy of Sciences of the United States of America, vol: 114, issue: 45, pages: E9740-E9749

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2017     |    DOI: https://doi.org/10.1073/pnas.1713050114

 

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

Jahn, Linda ; Schafhauser, Thomas ; Wibberg, Daniel ; Rückert, Christian ; Winkler, Anika ; Kulik, Andreas ; Weber, Tilmann ; Flor, Liane ; van Pée, Karl-Heinz ; Kalinowski, Jörn ; Ludwig-Müllera, Jutta ; Wohlleben, Wolfgang
in: Journal of Biotechnology, vol: 257, pages: 233-239

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2017     |    DOI: https://doi.org/10.1016/j.jbiotec.2017.06.410

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New developments on actinomyces CRISPR tools

Tong, Yaojun
Presented at:
DTU Biosustain Annual Seminar 2017

Type: Conference abstract for conference

Status: Published     |    Year: 2017

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plantiSMASH: automated identification, annotation and expression analysis of plant biosynthetic gene clusters

Kautsar, Satria A. ; Suarez Duran, Hernando G. ; Blin, Kai ; Osbourn, Anne ; Medema, Marnix H.
in: Nucleic acids research, vol: 45, issue: W1, pages: W55-W63

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2017     |    DOI: https://doi.org/10.1093/nar/gkx305

 

Polyketide Bioderivatization Using the Promiscuous Acyltransferase KirCII

Musiol-Kroll, Ewa Maria ; Zubeil, Florian ; Schafhauser, Thomas ; Härtner, Thomas ; Kulik, Andreas ; McArthur, John ; Koryakina, Irina ; Wohlleben, Wolfgang ; Grond, Stephanie ; Williams, Gavin J. ; Lee, Sang Yup ; Weber, Tilmann
in: A C S Synthetic Biology, vol: 6, issue: 3, pages: 421-427

Type: Letter (Peer reviewed)

Status: Published     |    Year: 2017     |    DOI: https://doi.org/10.1021/acssynbio.6b00341

 

Recent development of computational resources for new antibiotics discovery

Kim, Hyun Uk ; Blin, Kai ; Lee, Sang Yup ; Weber, Tilmann
in: Current opinion in Microbiology, vol: 39, pages: 113-120

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2017     |    DOI: https://doi.org/10.1016/j.mib.2017.10.027

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The aldehyde dehydrogenase, AldA, is essential for L-1,2-propanediol utilization in laboratory-evolved Escherichia coli

Aziz, Ramy K. ; Monk, Jonathan M. ; Andrews, Kathleen A. ; Nhan, Jenny ; Khaw, Valerie L. ; Wong, Hesper ; Palsson, Bernhard O. ; Charusanti, Pep
in: Microbiological Research, vol: 194, pages: 47-52

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2017     |    DOI: https://doi.org/10.1016/j.micres.2016.10.006

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

Alanjary, Mohammad ; Kronmiller, Brent ; Adamek, Martina ; Blin, Kai ; Weber, Tilmann ; Huson, Daniel ; Philmus, Benjamin ; Ziemert, Nadine
in: Nucleic acids research, vol: 45, pages: W42-W48

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2017     |    DOI: https://doi.org/10.1093/nar/gkx360

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

Blin, Kai ; Medema, Marnix H. ; Kottmann, Renzo ; Lee, Sang Yup ; Weber, Tilmann
in: Nucleic acids research, vol: 45, issue: D1, pages: D555-D559

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2017     |    DOI: https://doi.org/10.1093/nar/gkw960

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Towards systems metabolic engineering of streptomycetes for secondary metabolites production

Robertsen, Helene Lunde ; Weber, Tilmann ; Kim, Hyun Uk ; Lee, Sang Yup
in: Biotechnology Journal

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2017     |    DOI: https://doi.org/10.1002/biot.201700465

2016
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CRISPR/CAS9 based engineering of actinomycetal genomes

Weber, Tilmann ; Tong, Yaojun ; Lee, Sang Yup
Patent no.: WO2016150855, Date: 2016-09-29

Type: Patent

Status: Published     |    Year: 2016

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An Integrated Metabolomic and Genomic Mining Workflow to Uncover the Biosynthetic Potential of Bacteria

Månsson, Maria ; Vynne, Nikolaj Grønnegaard ; Klitgaard, Andreas ; Rasmussen, Jane Lind Nybo ; Melchiorsen, Jette ; D. Nguyen, Don ; Sanchez, Laura M. ; Ziemert, Nadine ; Dorrestein, Pieter C. ; Andersen, Mikael Rørdam ; Gram, Lone
in: mSystems, vol: 1, issue: 3

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2016     |    DOI: https://doi.org/10.1128/mSystems.00028-15

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Beauvericin counteracted multi-drug resistant Candida albicans by blocking ABC transporters

Tong, Yaojun ; Liu, Mei ; Zhang, Yu ; Liu, Xueting ; Huang, Ren ; Song, Fuhang ; Dai, Huanqin ; Ren, Biao ; Sun, Nuo ; Pei, Gang ; Bian, Jiang ; Jia, Xin-Ming ; Huang, Guanghua ; Zhou, Xuyu ; Li, Shaojie ; Zhang, Buchang ; Fukuda, Takashi ; Tomoda, Hiroshi ; Ōmura, Satoshi ; Cannon, Richard D. ; Calderone, Richard ; Zhang, Lixin
in: Synthetic and Systems Biotechnology, vol: 1, issue: 3, pages: 158-168

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2016     |    DOI: https://doi.org/10.1016/j.synbio.2016.10.001

 

Bioinformatics Tools for the Discovery of New Nonribosomal Peptides

Leclère, Valérie ; Weber, Tilmann ; Jacques, Philippe ; Pupin, Maude
part of: Nonribosomal Peptide and Polyketide Biosynthesis, pages: 209-232, 2016, Springer

Type: Book chapter (Peer reviewed)

Status: Published     |    Year: 2016     |    DOI: https://doi.org/10.1007/978-1-4939-3375-4_14

 

CRISPR technologies for bacterial systems: Current achievements and future directions

Choi, Kyeong Rok ; Lee, Sang Yup
in: Biotechnology Advances, vol: 34, issue: 7, pages: 1180-1209

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2016     |    DOI: https://doi.org/10.1016/j.biotechadv.2016.08.002

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CRISPy-web

Blin, Kai ; Pedersen, Lasse Ebdrup ; Weber, Tilmann ; Lee, Sang Yup
in: Synthetic and Systems Biotechnology, vol: 1, issue: 2, pages: 118-121

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2016     |    DOI: https://doi.org/10.1016/j.synbio.2016.01.003

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

Gallo, Giuseppe ; Renzone, Giovanni ; Palazzotto, Emilia ; Monciardini, Paolo ; Arena, Simona ; Faddetta, Teresa ; Giardina, Anna ; Alduina, Rosa ; Weber, Tilmann ; Sangiorgi, Fabio ; Russo, Alessandro ; Spinelli, Giovanni ; Sosio, Margherita ; Scaloni, Andrea ; Puglia, Anna Maria
in: B M C Genomics, vol: 17, issue: 42

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2016     |    DOI: https://doi.org/10.1186/s12864-016-2369-z

 

Engineering of actinomycetes using CRISPR/Cas9 technologies

Weber, Tilmann ; Tong, Yaojun ; Blin, Kai ; Lee, Sang Yup
in: Planta Medica, vol: 81, issue: S01
Presented at:
9th Joint Meeting of AFERP, ASP, GA, JSP, PSE & SIF

Type: Conference abstract in journal (Peer reviewed)

Status: Published     |    Year: 2016     |    DOI: https://doi.org/10.1055/s-0036-1596147

 

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

Iftime, Dumitrita ; Kulik, Andreas ; Härtner, Thomas ; Rohrer, Sabrina ; Niedermeyer, Timo Horst Johannes ; Stegmann, Evi ; Weber, Tilmann ; Wohlleben, Wolfgang
in: Journal of Industrial Microbiology and Biotechnology, vol: 43, issue: 2, pages: 277-291

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2016     |    DOI: https://doi.org/10.1007/s10295-015-1685-7

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

Weber, Tilmann
in: Synthetic and Systems Biotechnology, vol: 1, issue: 2, pages: 67-68

Type: Editorial (Peer reviewed)

Status: Published     |    Year: 2016     |    DOI: https://doi.org/10.1016/j.synbio.2016.04.001

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

Kim, Hyun Uk ; Charusanti, Pep ; Lee, Sang Yup ; Weber, Tilmann
in: Natural Product Reports, vol: 33, pages: 933-941

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2016     |    DOI: https://doi.org/10.1039/C6NP00019C

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Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking

Wang, Mingxun ; Carver, Jeremy J. ; Pevzner, Pavel ; Mohiman, Hosein ; Bandeira, Nuno ; Phelan, Vanessa V. ; Sanchez, Laura M. ; Garg, Neha ; Watrous, Jeramie ; Luzzatto-Knaa, Tal ; Frydenlund Michelsen, Charlotte ; Jelsbak, Lars ; Månsson, Maria ; Klitgaard, Andreas ; Nielsen, Kristian Fog
in: Nature Biotechnology, vol: 34, issue: 8, pages: 828-837

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2016     |    DOI: https://doi.org/10.1038/nbt.3597

 

Single walled carbon nanotube-based electrical biosensor for the label-free detection of pathogenic bacteria

Yoo, S. M. ; Baek, Y. K. ; Shin, S. ; Kim, J.H ; T. Jung, H. ; K. Choi, Y. ; Lee, Sang Yup
in: Journal of Nanoscience and Nanotechnology, vol: 16, issue: 6, pages: 6520-6525

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2016     |    DOI: https://doi.org/10.1166/jnn.2016.10882

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Ten Simple Rules for Taking Advantage of Git and GitHub

Perez-Riverol, Yasset ; Gatto, Laurent ; Wang, Rui ; Sachsenberg, Timo ; Uszkoreit, Julian ; Leprevost, Felipe da Veiga ; Fufezan, Christian ; Ternent, Tobias ; Eglen, Stephen J. ; Katz, Daniel S. ; Pollard, Tom J. ; Konovalov, Alexander ; Flight, Robert M. ; Blin, Kai ; Vizcaíno, Juan Antonio
in: P L o S Computational Biology (Online), vol: 12, issue: 7

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2016     |    DOI: https://doi.org/10.1371/journal.pcbi.1004947

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

Schafhauser, Thomas ; Kirchner, Norbert ; Kulik, Andreas ; Huijbers, Mieke M.E. ; Flor, Liane ; Caradec, Thibault ; Fewer, David P. ; Gross, Harald ; Jacques, Philippe ; Jahn, Linda ; Jokela, Jouni ; Leclère, Valérie ; Ludwig-Müller, Jutta ; Sivonen, Kaarina ; van Berkel, Willem J.H. ; Weber, Tilmann ; Wohlleben, Wolfgang ; van Pée, Karl-Heinz
in: Environmental Microbiology, vol: 18, issue: 11, pages: 3728–3741

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2016     |    DOI: https://doi.org/10.1111/1462-2920.13294

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The evolution of genome mining in microbes – a review

Ziemert, Nadine ; Alanjary, Mohammad ; Weber, Tilmann
in: Natural Product Reports, vol: 33, pages: 988-1005

Type: Review (Peer reviewed)

Status: Published     |    Year: 2016     |    DOI: https://doi.org/10.1039/C6NP00025H

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The secondary metabolite bioinformatics portal

Weber, Tilmann ; Kim, Hyun Uk
in: Synthetic and Systems Biotechnology, vol: 1, issue: 2, pages: 69-79

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2016     |    DOI: https://doi.org/10.1016/j.synbio.2015.12.002

2015
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antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters

Weber, Tilmann ; Blin, Kai ; Duddela, Srikanth ; Krug, Daniel ; Kim, Hyun Uk ; Bruccoleri, Robert ; Lee, Sang Yup ; Fischbach, Michael A. ; Müller, Rolf ; Wohlleben, Wolfgang
in: Nucleic acids research, vol: 43, issue: W1, pages: W237-W243

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2015     |    DOI: https://doi.org/10.1093/nar/gkv437

 

A systems approach to traditional oriental medicine

Kim, Hyun Uk ; Ryu, Jae Yong ; Lee, Jong Ok ; Lee, Sang Yup
in: Nature Biotechnology, vol: 33, issue: 3, pages: 264-268

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2015     |    DOI: https://doi.org/10.1038/nbt.3167

 

Biorefineries for the production of top building block chemicals and their derivatives

Choi, Sol ; Song, Chan Woo ; Shin, Jae Ho ; Lee, Sang Yup
in: Metabolic Engineering, vol: 28, pages: 223-239

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2015     |    DOI: https://doi.org/10.1016/j.ymben.2014.12.007

 

Combining Stable Isotope Labeling and Molecular Networking for Biosynthetic Pathway Characterization

Klitgaard, Andreas ; Nielsen, Jakob Blæsbjerg ; Frandsen, Rasmus John Normand ; Andersen, Mikael Rørdam ; Nielsen, Kristian Fog
in: Analytical Chemistry, vol: 87, issue: 13, pages: 6520-6526

Type: Journal article (Peer reviewed)

Status: E-pub ahead of print     |    Year: 2015     |    DOI: https://doi.org/10.1021/acs.analchem.5b01934

 

Combining UHPLC-High Resolution MS and Feeding of Stable Isotope Labeled Polyketide Intermediates for Linking Precursors to End Products

Klitgaard, Andreas ; Frandsen, Rasmus John Normand ; Holm, Dorte Koefoed ; Knudsen, Peter Boldsen ; Frisvad, Jens Christian ; Nielsen, Kristian Fog
in: Journal of Natural Products, vol: 78, issue: 7, pages: 1518-1525

Type: Journal article (Peer reviewed)

Status: E-pub ahead of print     |    Year: 2015     |    DOI: https://doi.org/10.1021/np500979d

 

CRISPR-Cas9 Based Engineering of Actinomycetal Genomes

Tong, Yaojun ; Charusanti, Pep ; Zhang, Lixin ; Weber, Tilmann ; Lee, Sang Yup
in: A C S Synthetic Biology, vol: 4, issue: 9, pages: 1020-1029

Type: Journal article (Peer reviewed)

Status: E-pub ahead of print     |    Year: 2015     |    DOI: https://doi.org/10.1021/acssynbio.5b00038

 

Design of homo-organic acid producing strains using multi-objective optimization

Kim, Tae Yong ; Park, Jong Myoung ; Kim, Hyun Uk ; Cho, Kwang Myung ; Lee, Sang Yup
in: Metabolic Engineering, vol: 28, pages: 63-73

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2015     |    DOI: https://doi.org/10.1016/j.ymben.2014.11.012

  PDF

Do genome-scale models need exact solvers or clearer standards?

Ebrahim, A. ; Almaas, E. ; Bauer, E. ; Bordbar, A. ; Burgard, A. P. ; Chang, R. L. ; Drager, A. ; Famili, I. ; Feist, A. M. ; Fleming, R. M. ; Fong, S. S. ; Hatzimanikatis, V. ; Herrgard, M. J. ; Holder, A. ; Hucka, M. ; Hyduke, D. ; Jamshidi, N. ; Lee, Sang Yup ; Le Novere, N. ; Lerman, J. A. ; Lewis, Nathan ; Ma, D. ; Mahadevan, R. ; Maranas, C. ; Nagarajan, H. ; Navid, A. ; Nielsen, Jens ; Nielsen, L. K. ; Nogales, J. ; Noronha, A. ; Pal, C. ; Palsson, Bernhard ; Papin, J. A. ; Patil, Kiran R. ; Price, N. D. ; Reed, J. L. ; Saunders, M. ; Senger, R. S. ; Sonnenschein, Nikolaus ; Sun, Yuekai ; Thiele, I.
in: Molecular Systems Biology, vol: 11, issue: 10

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2015     |    DOI: https://doi.org/10.15252/msb.20156157

 

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

Schafhauser, Thomas ; Wibberg, Daniel ; Rückert, Christian ; Winkler, Anika ; Flor, Liane ; van Pée, Karl-Heinz ; Fewer, David P. ; Sivonen, Kaarina ; Jahn, Linda ; Weber, Tilmann
in: Journal of Biotechnology, vol: 211, pages: 101-102

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2015     |    DOI: https://doi.org/10.1016/j.jbiotec.2015.07.004

 

How to set up collaborations between academia and industrial biotech companies

Pronk, Jack T. ; Lee, Sang Yup ; Lievense, Jeff ; Pierce, John ; Palsson, Bernhard ; Uhlén, Mathias ; Nielsen, Jens
in: Nature Biotechnology, vol: 33, issue: 3, pages: 237-240

Type: Comment/debate (Peer reviewed)

Status: Published     |    Year: 2015     |    DOI: https://doi.org/10.1038/nbt.3171

 

Human genes with a greater number of transcript variants tend to show biological features of housekeeping and essential genes

Ryu, Jae Yong ; Kim, Hyun Uk ; Lee, Sang Yup
in: Molecular BioSystems, vol: 11, issue: 10, pages: 2798-2807

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2015     |    DOI: https://doi.org/10.1039/c5mb00322a

  PDF

Liquid chromatography mass spectrometry for analysis of microbial metabolites

Klitgaard, Andreas

Type: Ph.D. thesis

Status: Published     |    Year: 2015

 

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

Weber, Tilmann ; Charusanti, Pep ; Musiol-Kroll, Ewa Maria ; Jiang, Xinglin ; Tong, Yaojun ; Kim, Hyun Uk ; Lee, Sang Yup
in: Trends in Biotechnology, vol: 33, issue: 1, pages: 15-26

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2015     |    DOI: https://doi.org/10.1016/j.tibtech.2014.10.009

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Minimum Information about a Biosynthetic Gene cluster

Medema, Marnix H. ; Kottmann, Renzo ; Yilmaz, Pelin ; Cummings, Matthew ; Biggins, John B. ; Blin, Kai ; de Bruijn, Irene ; Kim, Hyun Uk ; Nielsen, Jens ; Weber, Tilmann
in: Nature Chemical Biology, vol: 11, issue: 9, pages: 625-631

Type: Comment/debate (Peer reviewed)

Status: Published     |    Year: 2015     |    DOI: https://doi.org/10.1038/nchembio.1890

  PDF

Model-driven discovery of synergistic inhibitors against E. coli and S. enterica serovar Typhimurium targeting a novel synthetic lethal pair, aldA and prpC

Aziz, Ramy K. ; Khaw, Valerie L. ; Monk, Jonathan M. ; Brunk, Elizabeth ; Lewis, Robert ; Loh, Suh I. ; Mishra, Arti ; Nagle, Amrita A. ; Satyanarayana, Chitkala ; Dhakshinamoorthy, Saravanakumar ; Luche, Michele ; Kitchen, Douglas B. ; Andrews, Kathleen A. ; Palsson, Bernhard Ø ; Charusanti, Pep
in: Frontiers in Microbiology, vol: 6

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2015     |    DOI: https://doi.org/10.3389/fmicb.2015.00958

 

Multispot array combined with S1 nuclease-mediated elimination of unpaired nucleotides

Yoo, Seung Min ; Kim, Dong Min ; Lee, Sang Yup
in: BioChip Journal, vol: 9, issue: 2, pages: 156-163

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2015     |    DOI: https://doi.org/10.1007/s13206-015-9301-5

 

Recent advances in microbial production of fuels and chemicals using tools and strategies of systems metabolic engineering

Cho, Changhee ; Choi, So Young ; Luo, Zi Wei ; Lee, Sang Yup
in: Biotechnology Advances, vol: 33, issue: 7, pages: 1455-1466

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2015     |    DOI: https://doi.org/10.1016/j.biotechadv.2014.11.006

 

Reconstruction of genome-scale human metabolic models using omics data

Ryu, Jae Yong ; Kim, Hyun Uk ; Lee, Sang Yup
in: Integrative Biology, vol: 7, issue: 8, pages: 859-868

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2015     |    DOI: https://doi.org/10.1039/c5ib00002e

 

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

Iftime, Dumitrita ; Jasyk, Martin ; Kulik, Andreas ; Imhoff, Johannes F. ; Stegmann, Evi ; Wohlleben, Wolfgang ; Süssmuth, Roderich D. ; Weber, Tilmann
in: Chembiochem, vol: 16, issue: 18, pages: 2615-2623

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2015     |    DOI: https://doi.org/10.1002/cbic.201500377

 

Synergistic combinations of antifungals and antivirulence agents to fight against Candida albicans

Cui, Jinhui ; Ren, Biao ; Tong, Yaojun ; Dai, Huanqin ; Zhang, Lixin
in: Virulence, vol: 6, issue: 4, pages: 362-371

Type: Journal article (Peer reviewed)

Status: Accepted/In press     |    Year: 2015     |    DOI: https://doi.org/10.1080/21505594.2015.1039885

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Systems biology-guided identification of synthetic lethal gene pairs and its potential use to discover antibiotic combinations

Aziz, Ramy K. ; Monk, Jonathan M. ; Lewis, R. M. ; Loh, Suh I. ; Mishra, A. ; Nagle, A. A. ; Satyanarayana, C. ; Dhakshinamoorthy, S. ; Luche, M. ; Kitchen, D. B. ; Andrews, K. A. ; Fong, N. L. ; Li, H. J. ; Palsson, B. O. ; Charusanti, Pep
in: Scientific Reports, vol: 5

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2015     |    DOI: https://doi.org/10.1038/srep16025

 

Systems strategies for developing industrial microbial strains.

Lee, Sang Yup ; Kim, Hyun Uk
in: Nature Biotechnology, vol: 33, issue: 10, pages: 1061-1072

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2015     |    DOI: https://doi.org/10.1038/nbt.3365

2014
  PDF

Accurate Dereplication of Bioactive Secondary Metabolites from Marine-Derived Fungi by UHPLC-DAD-QTOFMS and a MS/HRMS Library

Kildgaard, Sara ; Mansson, Maria ; Dosen, Ina ; Klitgaard, Andreas ; Frisvad, Jens Christian ; Larsen, Thomas Ostenfeld ; Nielsen, Kristian Fog
in: Marine Drugs, vol: 12, pages: 3681-3705

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2014     |    DOI: https://doi.org/10.3390/md12063681

  PDF

Aggressive dereplication using UHPLC–DAD–QTOF: screening extracts for up to 3000 fungal secondary metabolites

Klitgaard, Andreas ; Iversen, Anita ; Andersen, Mikael Rørdam ; Larsen, Thomas Ostenfeld ; Frisvad, Jens Christian ; Nielsen, Kristian Fog
in: Analytical and Bioanalytical Chemistry, vol: 406, issue: 7, pages: 1933-1943

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2014     |    DOI: https://doi.org/10.1007/s00216-013-7582-x

  PDF

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

Bouhired, Sarah M. ; Crüsemann, Max ; Almeida, Celso ; Weber, Tilmann ; Piel, Jörn ; Schäberle, Till F. ; König, Gabriele M.
in: ChemBioChem, vol: 15, issue: 5, pages: 757-765

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2014     |    DOI: https://doi.org/10.1002/cbic.201300676

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Comparative Genomic and Metabolomic Analysis of Twelve Strains of Pseudoalteromonas luteoviolacea

Månsson, Maria ; Vynne, Nikolaj Grønnegaard ; Klitgaard, Andreas ; Melchiorsen, Jette ; Dorrestein, Pieter C. ; Gram, Lone
Presented at:
Gordon Conference on Marine Natural Products

Type: Poster (Peer reviewed)

Status: Published     |    Year: 2014

 

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

Stegmann, Evi ; Albersmeier, Andreas ; Spohn, Marius ; Gert, Helena ; Weber, Tilmann ; Wohlleben, Wolfgang ; Kalinowski, Jörn ; Rückert, Christian
in: Journal of Biotechnology, vol: 189, pages: 46-47

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2014     |    DOI: https://doi.org/10.1016/j.jbiotec.2014.08.034

 

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, Tilmann
in: Genome Announcements, vol: 2, issue: 1, pages: e01198-13

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2014     |    DOI: https://doi.org/10.1128/genomeA.01198-13

 

Effects of introducing heterologous pathways on microbial metabolism with respect to metabolic optimality

Kim, Hyun Uk ; Kim, Byoungjin ; Seung, Do Young ; Yup Lee, Sang
in: Biotechnology and Bioprocess Engineering, vol: 19, issue: 4, pages: 660-667

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2014     |    DOI: https://doi.org/10.1007/s12257-014-0137-y

 

Engineering synergy in biotechnology

Nielsen, Jens ; Fussenegger, Martin ; Keasling, Jay ; Yup Lee, Sang ; Liao, James C. ; Prather, Kristala ; Palsson, Bernhard
in: Nature Chemical Biology, vol: 10, issue: 5, pages: 319-322

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2014     |    DOI: https://doi.org/10.1038/nchembio.1519

 

Genome Mining for antibiotics biosynthesis pathways with antiSMASH 3

Weber, Tilmann ; Kim, Hyun Uk ; Blin, Kai ; Takano, Eriko ; Breitling, Rainer ; Medema, Marnix
part of: Abstract Book - DTU Sustain Conference 2014, 2014, Technical University of Denmark, Kgs. Lyngby
Presented at:
DTU Sustain Conference 2014

Type: Conference abstract in proceedings (Peer reviewed)

Status: Published     |    Year: 2014

  PDF

Improved lanthipeptide detection and prediction for antiSMASH

Blin, Kai ; Kazempour, Daniyal ; Wohlleben, Wolfgang ; Weber, Tilmann
in: P L o S One, vol: 9, issue: 2

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2014     |    DOI: https://doi.org/10.1371/journal.pone.0089420

 

In silico tools for the analysis of antibiotic biosynthetic pathways.

Weber, Tilmann
in: International Journal of Medical Microbiology, vol: 304, pages: 230-235

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2014     |    DOI: https://doi.org/10.1016/j.ijmm.2014.02.001

 

KirCII- promising tool for polyketide diversification

Musiol-Kroll, Ewa Maria ; Härtner, Thomas ; Kulik, Andreas ; Wohlleben, Wolfgang ; Weber, Tilmann ; Lee, Sang Yup
part of: Abstract Book - DTU Sustain Conference 2014, 2014, Technical University of Denmark, Kgs. Lyngby
Presented at:
DTU Sustain Conference 2014

Type: Conference abstract in proceedings (Peer reviewed)

Status: Published     |    Year: 2014

  PDF

Novel Amycolatopsis balhimycina biochemical abilities unveiled by proteomics

Alduina, R. ; Gallo, G. ; Renzone, G. ; Weber, Tilmann ; Scaloni, A. ; Puglia, A. M.
in: F E M S Microbiology Letters, vol: 351, pages: 209-215

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2014     |    DOI: https://doi.org/10.1111/1574-6968.12324

 

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

Ye, Zhixia ; Musiol-Kroll, Ewa Maria ; Weber, Tilmann ; Williams, Gavin J.
in: Chemistry & Biology, vol: 21, pages: 636-646

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2014     |    DOI: https://doi.org/10.1016/j.chembiol.2014.02.019

 

Systems biology and biotechnology of Streptomyces species for the production of secondary metabolites

Hwang, Kyu-Sang ; Kim, Hyun Uk ; Charusanti, Pep ; Palsson, Bernhard ; Yup Lee, Sang
in: Biotechnology Advances, vol: 32, issue: 2, pages: 255-268

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2014     |    DOI: https://doi.org/10.1016/j.biotechadv.2013.10.008

2013
 

Accurate prediction of secondary metabolite gene clusters in filamentous fungi.

Andersen, Mikael Rørdam ; Nielsen, Jakob Blæsbjerg ; Klitgaard, Andreas ; Petersen, Lene Maj ; Zachariasen, Mia ; Hansen, Tilde J ; Holberg Blicher, Lene ; Gotfredsen, Charlotte Held ; Larsen, Thomas Ostenfeld ; Nielsen, Kristian Fog ; Mortensen, Uffe Hasbro
in: Proceedings of the National Academy of Sciences of the United States of America, vol: 110, issue: 1, pages: E99-E107

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2013     |    DOI: https://doi.org/10.1073/pnas.1205532110

 

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

Blin, Kai ; Medema, Marnix H. ; Kazempour, Daniyal ; Fischbach, Michael ; Breitling, Rainer ; Takano, Eriko ; Weber, Tilmann
in: Nucleic acids research, vol: 41, issue: W1, pages: W204-W212

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2013     |    DOI: https://doi.org/10.1093/nar/gkt449

 

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, Ewa Maria ; Blin, K. ; Wohlleben, W. ; Pühler, A. ; Kalinowski, J. ; Weber, Tilmann
in: Journal of biotechnology, vol: 168, pages: 739-740

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2013     |    DOI: https://doi.org/10.1016/j.jbiotec.2013.10.004