Publications

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2019
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Breaking the state-of-the-art in the chemical industry with new-to-Nature products via synthetic microbiology

Martinelli, Laura ; Nikel, Pablo Ivan
in: Microbial Biotechnology, vol: 12, issue: 2, pages: 187-190

Type: Editorial (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1111/1751-7915.13372

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Building a global alliance of biofoundries

Hillson, Nathan ; Caddick, Mark ; Cai, Yizhi ; Carrasco, Jose A. ; Chang, Matthew Wook ; Curach, Natalie C. ; Bell, David J. ; Le Feuvre, Rosalind ; Friedman, Douglas C. ; Fu, Xiongfei ; Gold, Nicholas D. ; Herrgård, Markus J. ; Holowko, Maciej B. ; Johnson, James R. ; Johnson, Richard A. ; Keasling, Jay D. ; Kitney, Richard I. ; Kondo, Akihiko ; Liu, Chenli ; Martin, Vincent J.J. ; Menolascina, Filippo ; Ogino, Chiaki ; Patron, Nicola J. ; Pavan, Marilene ; Poh, Chueh Loo ; Pretorius, Isak S. ; Rosser, Susan J. ; Scrutton, Nigel S. ; Storch, Marko ; Tekotte, Hille ; Travnik, Evelyn ; Vickers, Claudia E. ; Yew, Wen Shan ; Yuan, Yingjin ; Zhao, Huimin ; Freemont, Paul S.
in: Nature Communications, vol: 10

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1038/s41467-019-10079-2

 

Cell factory engineering for improved production of natural products

Nielsen, Jens
in: Natural Product Reports

Type: Journal article (Peer reviewed)

Status: Accepted/In press     |    Year: 2019     |    DOI: https://doi.org/10.1039/c9np00005d

 

Cellular responses to reactive oxygen species are predicted from molecular mechanisms

Yang, Laurence ; Mih, Nathan ; Anand, Amitesh ; Park, Joon Ho ; Tan, Justin ; Yurkovich, James T. ; Monk, Jonathan M. ; Lloyd, Colton J. ; Sandberg, Troy E. ; Seo, Sang Woo ; Kim, Donghyuk ; Sastry, Anand V. ; Phaneuf, Patrick ; Gao, Ye ; Broddrick, Jared T. ; Chen, Ke ; Heckmann, David ; Szubin, Richard ; Hefner, Ying ; Feist, Adam M. ; Palsson, Bernhard O.
in: Proceedings of the National Academy of Sciences of the United States of America, vol: 116, issue: 28, pages: 14368-14373

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1073/pnas.1905039116

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Changing substrate specificity and iteration of amino acid chain elongation in glucosinolate biosynthesis through targeted mutagenesis of Arabidopsis methylthioalkylmalate synthase 1

Petersen, Annette ; Gram Hansen, Lea ; Mirza, Nadia ; Crocoll, Christoph ; Mirza, Osman ; Halkier, Barbara Ann
in: Bioscience Reports, vol: 39, issue: 7

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1042/BSR20190446

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Characterization of CA-MRSA TCH1516 exposed to nafcillin in bacteriological and physiological media

Poudel, Saugat ; Tsunemoto, Hannah ; Meehan, Michael ; Szubin, Richard ; Olson, Connor A. ; Lamsa, Anne ; Seif, Yara ; Dillon, Nicholas ; Vrbanac, Alison ; Sugie, Joseph ; Dahesh, Samira ; Monk, Jonathan M. ; Dorrestein, Pieter C. ; Pogliano, Joseph ; Knight, Rob ; Nizet, Victor ; Palsson, Bernhard O. ; Feist, Adam M.
in: Scientific Data, vol: 6, issue: 1

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1038/s41597-019-0051-4

 

Characterization of Hypermutator Pseudomonas aeruginosa Isolates from Patients with Cystic Fibrosis in Australia

Rees, Vanessa Emily ; Deveson Lucas, Deanna S. ; López-Causapé, Carla ; Huang, Yuling ; Kotsimbos, Tom ; Bulitta, Jürgen B. ; Rees, Murray C. ; Barugahare, Adele ; Peleg, Anton Y. ; Nation, Roger L. ; Oliver, Antonio ; Boyce, John D. ; Landersdorfer, Cornelia B.
in: Antimicrobial Agents and Chemotherapy, pages: e02538-18

Type: Journal article (Peer reviewed)

Status: Accepted/In press     |    Year: 2019     |    DOI: https://doi.org/10.1128/AAC.02538-1

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Chasing bacterial chassis for metabolic engineering: a perspective review from classical to non-traditional microorganisms

Calero, Patricia ; Nikel, Pablo I.
in: Microbial Biotechnology, vol: 12, issue: 1, pages: 98-124

Type: Review (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1111/1751-7915.13292

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Chromophore pre-maturation for improved speed and sensitivity of split-GFP monitoring of protein secretion

Lundqvist, Magnus ; Thalén, Niklas ; Volk, Anna Luisa ; Hansen, Henning Gram ; von Otter, Eric ; Nygren, Per-Åke ; Uhlén, Mathias ; Rockberg, Johan
in: Scientific Reports, vol: 9, issue: 1

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1038/s41598-018-36559-x

 

Classification and enzyme kinetics of formate dehydrogenases for biomanufacturing via CO2 utilization

Nielsen, Christian Førgaard ; Lange, Lene ; Meyer, Anne S.
in: Biotechnology Advances

Type: Journal article (Peer reviewed)

Status: Accepted/In press     |    Year: 2019     |    DOI: https://doi.org/10.1016/j.biotechadv.2019.06.007

 

Cocktails of human monoclonal IgG antibodies capable of neutralizing dendrotoxin-mediated neurotoxicity of black mamba venom in vivo

Laustsen, Andreas H. ; Karatt-Vellatt, Aneesh ; Masters, Edward W. ; Arias, Ana Silvia ; Pus, Urska ; Knudsen, Cecilie ; Oscoz, Saioa ; Slavny, Peter ; Griffiths, Daniel T. ; Luther, Alice M. ; Leah, Rachael A. ; Lindholm, Majken ; Lomonte, Bruno ; Mar a Guti rrez, Jos ; McCafferty, John
in: Toxicon, vol: 159, issue: Supp. 1, pages: S5-S6
Presented at:
19th EU-IST Congress

Type: Conference abstract in journal (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1016/j.toxicon.2018.11.331

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Collateral sensitivity constrains resistance evolution of the CTX-M-15 β-lactamase

Rosenkilde, Carola Elisa Heesemann ; Munck, Christian ; Porse, Andreas ; Linkevicius, Marius ; Andersson, Dan I. ; Sommer, Morten Otto Alexander
in: Nature Communications, vol: 10

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1038/s41467-019-08529-y

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Combating viral contaminants in CHO cells by engineering innate immunity

Chiang, Austin W.T. ; Li, Shangzhong ; Kellman, Benjamin P. ; Chattopadhyay, Gouri ; Zhang, Yaqin ; Kuo, Chih Chung ; Gutierrez, Jahir M. ; Ghazi, Faezeh ; Schmeisser, Hana ; Ménard, Patrice ; Petersen Bjørn, Sara ; Voldborg, Bjørn Gunnar ; Rosenberg, Amy S. ; Puig, Montserrat ; Lewis, Nathan E.
in: Scientific Reports, vol: 9, issue: 1

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1038/s41598-019-45126-x

 

Combined Rapid Injection NMR and Simulation Approach to Probe Redox-Dependent Pathway Control in Living Cells

Jensen, Pernille Rose ; Matos, Marta ; Sonnenschein, Nikolaus ; Meier, Sebastian
in: Analytical Chemistry, vol: 91, issue: 8, pages: 5395-5402

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1021/acs.analchem.9b00660

 

Combining Pro-peptide Engineering and Multisite Saturation Mutagenesis to Improve the Catalytic Potential of Keratinase

Su, Chang ; Gong, Jin Song ; Sun, Yu Xin ; Qin, Jiufu ; Zhai, Shen ; Li, Heng ; Li, Hui ; Lu, Zhen Ming ; Xu, Zheng Hong ; Shi, Jin Song
in: A C S Synthetic Biology, vol: 8, issue: 2, pages: 425-433

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1021/acssynbio.8b00442

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Comparative Transcriptome Analysis Shows Conserved Metabolic Regulation during Production of Secondary Metabolites in Filamentous Fungi

Nielsen, Jens ; Prigent, Sylvain ; Grijseels, Sietske ; Workman, Mhairi ; Ji, Boyang
in: mSystems, vol: 4, issue: 2

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1128/mSystems.00012-19

 

Complete biosynthesis of cannabinoids and their unnatural analogues in yeast

Luo, Xiaozhou ; Reiter, Michael A. ; d’Espaux, Leo ; Wong, Jeff ; Denby, Charles M. ; Lechner, Anna ; Zhang, Yunfeng ; Grzybowski, Adrian T. ; Harth, Simon ; Lin, Weiyin ; Lee, Hyunsu ; Yu, Changhua ; Shin, John ; Deng, Kai ; Benites, Veronica T. ; Wang, George ; Baidoo, Edward E.K. ; Chen, Yan ; Dev, Ishaan ; Petzold, Christopher J. ; Keasling, Jay D.
in: Nature, vol: 567, issue: 7746, pages: 123-126

Type: Letter (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1038/s41586-019-0978-9

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Computational methods for microbial cell factory engineering aided by evolution

Jensen, Kristian

Type: Ph.D. thesis

Status: Published     |    Year: 2019

 

Construction of mini-chemostats for high-throughput strain characterization

Bergenholm, David ; Liu, Guodong ; Hansson, David ; Nielsen, Jens
in: Biotechnology and Bioengineering, vol: 116, issue: 5, pages: 1029-1038

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1002/bit.26931

 

Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0

Heirendt, Laurent ; Arreckx, Sylvain ; Pfau, Thomas ; Mendoza, Sebastian N. ; Richelle, Anne ; Heinken, Almut ; Haraldsdottir, Hulda S. ; Wachowiak, Jacek ; Keating, Sarah M. ; Vlasov, Vanja ; Magnusdottir, Stefania ; Ng, Chiam Yu ; Preciat, German ; Zagare, Alise ; Chan, Siu Hung Joshua ; Aurich, Maike K. ; Clancy, Catherine M. ; Modamio, Jennifer ; Sauls, John T. ; Noronha, Alberto ; Bordbar, Aarash ; Cousins, Benjamin ; El Assal, Diana C. ; Valcarcel, Luis V. ; Apaolaza, Inigo ; Ghaderi, Susan ; Ahookhosh, Masoud ; Ben Guebila, Marouen ; Kostromins, Andrejs ; Sompairac, Nicolas ; Le, Hoai M. ; Ma, Ding ; Sun, Yuekai ; Wang, Lin ; Yurkovich, James T. ; Oliveira, Miguel A. P. ; Vuong, Phan T. ; El Assal, Lemmer P. ; Kuperstein, Inna ; Zinovyev, Andrei ; Hinton, H. Scott ; Bryant, William A. ; Aragon Artacho, Francisco J. ; Planes, Francisco J. ; Stalidzans, Egils ; Maass, Alejandro ; Vempala, Santosh ; Hucka, Michael ; Saunders, Michael A. ; Maranas, Costas D. ; Lewis, Nathan E. ; Sauter, Thomas ; Palsson, Bernhard O. ; Thiele, Ines ; Fleming, Ronan M. T.
in: Nature Protocols, vol: 14, issue: 3, pages: 639-702

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1038/s41596-018-0098-2

 

CRISPR/Cas9 as a Genome Editing Tool for Targeted Gene Integration in CHO Cells

Sergeeva, Daria ; Manuel Camacho Zaragoza, Jose ; Lee, Jae Seong ; Kildegaard, Helene Faustrup
part of: CRISPR Gene Editing, pages: 213-232, 2019

Type: Book chapter (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1007/978-1-4939-9170-9_13

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CRISPR/Cas9-RNAi system for combinatorial metabolic engineering of Saccharomyces cerevisiae

Kildegaard, Kanchana Rueksomtawin ; Ribeiro Ramos Tramontin, Larissa ; Chekina, Ksenia ; Li, Mingji ; Goedecke, Tobias Justus ; Kristensen, Mette ; Borodina, Irina
in: Yeast, vol: 36, issue: 5, pages: 237-247

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1002/yea.3390

 

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

 

CRISPR Toolbox for Mammalian Cell Engineering

Sergeeva, Daria ; Julie la Cour Karottki, Karen ; Lee, Jae Seong ; Kildegaard, Helene Faustrup
part of: Cell Culture Engineering: Recombinant Protein Production, 2019

Type: Book chapter (Peer reviewed)

Status: Published     |    Year: 2019