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2023

antiSMASH 7.0

Blin, Kai ; Shaw, Simon ; Augustijn, Hannah E ; Reitz, Zachary L ; Biermann, Friederike ; Alanjary, Mohammad ; Fetter, Artem ; Terlouw, Barbara R ; Metcalf, William W ; Helfrich, Eric J N ; van Wezel, Gilles P ; Medema, Marnix H ; Weber, Tilmann
in: Nucleic Acids Research

Type: Journal article (Peer reviewed)

Status: Accepted/In press | Year: 2023 | DOI: https://doi.org/10.1093/nar/gkad344

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Embryogenesis of a calanoid copepod analyzed by transcriptomics

Acebal, Miguel Cifuentes ; Dalgaard, Louise Torp ; Jørgensen, Tue Sparholt ; Hansen, Benni Winding
in: Comparative Biochemistry and Physiology - Part D: Genomics and Proteomics, vol: 45

Type: Journal article (Peer reviewed)

Status: Published | Year: 2023 | DOI: https://doi.org/10.1016/j.cbd.2022.101054

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Extraction and Oxford Nanopore sequencing of genomic DNA from filamentous Actinobacteria

Alvarez-Arevalo, Maria ; Sterndorff, Eva Baggesgaard ; Faurdal, David ; Jørgensen, Tue Sparholt ; Mourched, Anna-Sophie ; Vuksanovic, Oliwia ; Saha, Subhasish ; Weber, Tilmann
in: STAR Protocols, vol: 4, issue: 1

Type: Journal article (Peer reviewed)

Status: Published | Year: 2023 | DOI: https://doi.org/10.1016/j.xpro.2022.101955

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Identification and heterologous expression of the globomycin biosynthetic gene cluster

Oves-Costales, Daniel ; Gren, Tetiana ; Sterndorff, Eva Baggesgaard ; Martín, Jesús ; Ortiz-López, Francisco Javier ; Jørgensen, Tue S. ; Jiang, Xinglin ; Román-Hurtado, Fernando ; Reyes, Fernando ; Genilloud, Olga ; Weber, Tilmann
in: Synthetic and Systems Biotechnology, vol: 8, issue: 2, pages: 206-212

Type: Journal article (Peer reviewed)

Status: Published | Year: 2023 | DOI: https://doi.org/10.1016/j.synbio.2023.02.001

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MIBiG 3.0: a community-driven effort to annotate experimentally validated biosynthetic gene clusters

Terlouw, Barbara R ; Blin, Kai ; Navarro-Muñoz, Jorge C ; Avalon, Nicole E ; Chevrette, Marc G ; Egbert, Susan ; Lee, Sanghoon ; Meijer, David ; Recchia, Michael J J ; Reitz, Zachary L ; van Santen, Jeffrey A ; Selem-Mojica, Nelly ; Tørring, Thomas ; Zaroubi, Liana ; Alanjary, Mohammad ; Aleti, Gajender ; Aguilar, César ; Al-Salihi, Suhad A A ; Augustijn, Hannah E ; Avelar-Rivas, J Abraham ; Avitia-Domínguez, Luis A ; Barona-Gómez, Francisco ; Bernaldo-Agüero, Jordan ; Bielinski, Vincent A ; Biermann, Friederike ; Booth, Thomas J ; Carrion Bravo, Victor J ; Castelo-Branco, Raquel ; Chagas, Fernanda O ; Cruz-Morales, Pablo ; Du, Chao ; Duncan, Katherine R ; Gavriilidou, Athina ; Gayrard, Damien ; Gutiérrez-García, Karina ; Haslinger, Kristina ; Helfrich, Eric J N ; van der Hooft, Justin J J ; Jati, Afif P ; Kalkreuter, Edward ; Kalyvas, Nikolaos ; Kang, Kyo B ; Kautsar, Satria ; Kim, Wonyong ; Kunjapur, Aditya M ; Li, Yong-Xin ; Lin, Geng-Min ; Loureiro, Catarina ; Louwen, Joris J R ; Louwen, Nico L L ; Lund, George ; Parra, Jonathan ; Philmus, Benjamin ; Pourmohsenin, Bita ; Pronk, Lotte J U ; Rego, Adriana ; Rex, Devasahayam Arokia Balaya ; Robinson, Serina ; Rosas-Becerra, L Rodrigo ; Roxborough, Eve T ; Schorn, Michelle A ; Scobie, Darren J ; Singh, Kumar Saurabh ; Sokolova, Nika ; Tang, Xiaoyu ; Udwary, Daniel ; Vigneshwari, Aruna ; Vind, Kristiina ; Vromans, Sophie P J M ; Waschulin, Valentin ; Williams, Sam E ; Winter, Jaclyn M ; Witte, Thomas E ; Xie, Huali ; Yang, Dong ; Yu, Jingwei ; Zdouc, Mitja ; Zhong, Zheng ; Collemare, Jérôme ; Linington, Roger G ; Weber, Tilmann ; Medema, Marnix H
in: Nucleic Acids Research, vol: 51, issue: D1, pages: D603–D610

Type: Journal article (Peer reviewed)

Status: Published | Year: 2023 | DOI: https://doi.org/10.1093/nar/gkac1049

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Properties of Multidrug-Resistant Mutants Derived from Heterologous Expression Chassis Strain Streptomyces albidoflavus J1074

Dolya, Borys ; Hryhorieva, Olena ; Sorochynska , Khrystyna ; Lopatniuk , Maria ; Ostash , Iryna ; Tseduliak , Vasylyna-Marta ; Sterndorff, Eva Baggesgaard ; Jørgensen, Tue Sparholt ; Gren, Tetiana ; Dacyuk, Yuriy ; Weber, Tilmann ; Luzhetskyy , Andriy ; Fedorenko, Victor ; Ostash, Bohdan
in: Microorganisms, vol: 11

Type: Journal article (Peer reviewed)

Status: Published | Year: 2023 | DOI: https://doi.org/10.3390/microorganisms11051176

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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

Jørgensen, Tue Sparholt ; Pedersen, Martin Schou ; Blin, Kai ; Kuntke, Franziska ; Salling, Henrik K ; Marvig, Rasmus L. ; Michaelsen, Thomas Y ; Albertsen, Mads ; Larsen, Helene
in: Journal of Virological Methods, vol: 312

Type: Journal article (Peer reviewed)

Status: Published | Year: 2023 | DOI: https://doi.org/10.1016/j.jviromet.2022.114648

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UmetaFlow

Kontou, Eftychia E. ; Walter, Axel ; Alka, Oliver ; Pfeuffer, Julianus ; Sachsenberg, Timo ; Mohite, Omkar S. ; Nuhamunada, Matin ; Kohlbacher, Oliver ; Weber, Tilmann
in: Journal of Cheminformatics, vol: 15

Type: Journal article (Peer reviewed)

Status: Published | Year: 2023 | DOI: https://doi.org/10.1186/s13321-023-00724-w

2022

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A Versatile in Vivo DNA Assembly Toolbox for Fungal Strain Engineering

Jarczynska, Zofia Dorota ; Garcia Vanegas, Katherina ; Deichmann, Marcus ; Nørskov Jensen, Christina ; Scheeper, Marouschka Jasmijn ; Futyma, Malgorzata Ewa ; Strucko, Tomas ; Jares Contesini, Fabiano ; Sparholt Jørgensen, Tue ; Blæsbjerg Hoof, Jakob ; Hasbro Mortensen, Uffe
in: ACS Synthetic Biology, vol: 11, issue: 10, pages: 3251-3263

Type: Journal article (Peer reviewed)

Status: Published | Year: 2022 | DOI: https://doi.org/10.1021/acssynbio.2c00159

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Complete Genome Sequence of the Collinolactone Producer Streptomyces sp. Strain Go40/10

Sterndorff, Eva Baggesgaard ; Jørgensen, Tue Sparholt ; Garzon, Jaime Felipe Guerrero ; Schmid, Julian C. ; Grond, Stephanie ; Weber, Tilmann
in: Microbiology Resource Announcements, vol: 11, issue: 8

Type: Journal article

Status: Published | Year: 2022 | DOI: https://doi.org/10.1128/mra.00220-22